Essential Medical Genetics

Höfundar: Edward S. Tobias, Michael Connor, Malcolm Ferguson Smith (Útgáfa: 1)
Essential Medical Genetics

Kaup valmöguleikar

Essential Medical Genetics gives a balanced introduction to the basic principles of genetics and how it is applied to the understanding and treatment of diseases with a genetic component. Divided into three sections, basic principles, common situations in clinical genetics, and electronic databases, it covers all the information that medical students are taught at both preclinical and clinical level.

Nánar um bókina

Útgefandi
Wiley Global Research (STMS)
ISBN
9781444394818
Print ISBN
9781405169745
Format
ePub
Útgáfa
1
Höfundar
Edward S. Tobias, Michael Connor, Malcolm Ferguson Smith
Tungumál
English
Útgefið
3/11/2011
Prent takmörkun á líftíma
100
Prent takmörkun
10
Afritunar takmörkun
2

Kaflar

  • Front Matter
  • Preface
  • Acknowledgements
  • How to get the best out of your textbook
  • An interactive textbook
  • A companion website
  • Features contained within your textbook
  • Part 1 Basic Principles
  • CHAPTER 1 Medical genetics in perspective
  • Key Topics
  • Introduction
  • Table 1.1 Some important landmarks in the development of medical genetics
  • Scientific basis of medical genetics
  • Mendel’s contribution
  • Fig. 1.1 Example of Mendel’s breeding experiments for a single trait (yellow or green peas).
  • Fig. 1.2 Example of Mendel’s breeding experiments for a single trait (round or wrinkled peas).
  • Fig. 1.3 Example of Mendel’s breeding experiments for two traits (yellow or green and round or wrinkled peas).
  • Chromosomal basis of inheritance
  • Chemical basis of inheritance
  • Chromosomal disorders
  • Fig. 1.4 Diagram displayed on the DECIPHER website (at http://decipher.sanger.ac.uk/syndromes) indicating chromosomal loci associated with known clinical syndromes. Reproduced with permission from the Wellcome Trust Sanger Institute. Flicek et al. (2010) Nucleic Acids Res 38 (Database issue):D557–62.
  • Mitochondrial disorders
  • Single-gene disorders
  • Table 1.2 Human genes and single-gene traits (see McKusick, 2007, and the OMIM database)
  • Fig. 1.5 (a) Transcript structure of the 38-exon CHARGE association gene, CHD7, on human chromosome 8. (b) DNA sequence of the first coding exon (containing the start codon). The DNA sequence displayed in purple is the untranslated region of this exon, immediately preceding the ATG start codon. (c) Protein features of CHD7, as predicted by the different computer programs (e.g. SMART) shown on the left. Reproduced with permission from the Ensembl database at the Wellcome Trust Sanger Institute. Flicek et al. (2010) Ensembl’s 10th year. Nucleic Acids Res 38 (Database issue):D557–62. See Chapter 19.
  • Multifactorial (part-genetic) disorders
  • Somatic cell genetic (cumulative genetic) disorders
  • Clinical applications of medical genetics
  • Genetic assessment and management
  • Treatment and prevention of genetic disease
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • CHAPTER 2 The human genome
  • Key Topics
  • Introduction
  • Structure and organisation of the genome
  • Gene identification
  • The Human Genome Project
  • How it was carried out
  • Total gene numbers
  • Recently described RNA gene classes
  • Table 2.1 Types of RNA
  • Uses of the Human Genome Project data and ways of accessing it
  • Fig. 2.1 A Homo sapiens genome browser display page at Ensembl. This can be reached via the search page at http://www.ensembl.org/Homo_sapiens/index.html. The same region as that shown in the UCSC genome browser example in Fig. 2.3 is displayed. This can be revealed by typing the nucleotide boundaries of the region directly into the sequence position boxes in the H. sapiens browser window, shown in Fig. 2.2. Reproduced with permission from the Wellcome Trust Sanger Institute. Flicek et al. (2010) Ensembl’s 10th year. Nucleic Acids Res 38 (Database issue):D557–62.
  • Fig. 2.2 The H. sapiens browser window of Ensembl. The latest version of this page can be accessed at http://www.ensembl.org/Homo_sapiens/index.html. Reproduced with permission from the Wellcome Trust Sanger Institute. Flicek et al. (2010) Ensembl’s 10th year. Nucleic Acids Res 38 (Database issue):D557–62.
  • Fig. 2.3 The human data search page of the UCSC genome browser. The window shows the display of all identified genes within a specific chromosomal band. In (a), the genes located within Xp21.3 are shown, after opening the UCSC Genome Browser at http://genome.ucsc.edu/cgi-bin/hgGateway, typing the cytogenetic band name into the ‘position or search term’ and pressing ‘submit’(b). Alternatively, a precise region could have been defined by the flanking nucleotide positions (counted from the telomere of the p arm) or by specific genetic markers. Kent et al. (2002) The human genome browser at UCSC. Genome Res.12(6):996–1006.
  • Remaining uncertainties
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • CHAPTER 3 Nucleic acid structure and function
  • Key Topics
  • Introduction
  • Nucleic acid structure
  • Fig. 3.1 Diagram of nucleic acid structure. The 5′ phosphate end is at the top and the 3′ hydroxyl group is at the bottom of the molecule.
  • Fig. 3.2 Chemical structure of purines, pyrimidines, ribose, deoxyribose and the 5′ to 3′ phosphate linkage. The hydrogen bonds betwe en adenine and thymine (or uracil) and between guanine and cytosine are indicated.
  • Fig. 3.3 Diagram of a DNA double helix.
  • Table 3.1 Proportions of different types of nuclear DNA
  • Fig. 3.4 Sequence of a CA microsatellite DNA marker (named AFMB044XE9 or D6S1615; shown in coloured upper case letters) and its flanking DNA (shown in black lower case letters) from the UCSC (University of California, Santa Cruz) database (see Chapter 19). The (CA)n repeat itself can be seen within the genomic sequence shown on lines 4 and 5. The blue letters represent computer-predicted putative splice sites (probably erroneous) and the lower case letters on lines 4 and 5 represent bases that are present in the latest database version but were absent in a different version.
  • Table 3.2 The genetic code with codons shown as messenger RNA (5′ → 3′) The corresponding DNA codons are complementary.
  • Nucleic acid function
  • Table 3.3 Examples of genes and their protein products
  • Fig. 3.5 Genomic nucleotide sequence of the human β-globin gene. The sequence of the primary gene transcript is shown in the 5′ to 3′ direction, with T in place of U. The 5′ and 3′ untranslated regions (UTRs) are represented in purple and the untranscribed upstream and downstream sequences are displayed in green. Letters shown in capitals, black or blue represent sequences corresponding to the mature mRNA, coding sequence and two introns, respectively. The CCAAT box within the promoter is highlighted in blue. From the exon display of transcript ENST00000335295 in Ensembl release 44 at http://www.ensembl.org as discussed in Chapter 19.
  • Fig. 3.6 Diagram of transcription, mRNA processing and translation. By convention, the 5′ end of the mRNA molecule is placed to the left.
  • Fig. 3.7 Post-translational modification of insulin.
  • Gene regulation
  • Fig. 3.8 The human β-globin gene, indicating some of the adjacent sequences involved in the regulation of transcription. The leader (5’ UTR) and trailer (3’ UTR) sequences are also shown.
  • DNA replication
  • Fig. 3.9 Initiation of replication.
  • Fig. 3.10 Semiconservative replication.
  • Fig. 3.11 Harlequin chromosomes (BrdU staining)
  • Mutation types, effects and nomenclature
  • Length mutations
  • Fig. 3.12 Unequal recombination in the colour vision gene cluster resulting in loss of genes or creation of fused hybrid genes with altered action spectrums.
  • Table 3.4 Examples of DNA mutation
  • Fig. 3.13 Diagram to compare normal recombination (left) with gene conversion (right).
  • Fig. 3.14 DNA analysis of a family with myotonic dystrophy. Note the instability of the larger mutant allele, represented by the upper band, with decreasing mobility through the electrophoresis gel (from top to bottom) in successive generations.
  • Point mutations
  • Fig. 3.15 Examples of DNA repair mechanisms. Note that in nucleotide excision repair (NER), the exonucleases remove a stretch of nucleotides, including the altered bases. In base excision repair (BER), in contrast, only the altered base (and its sugar phosphate) is removed.
  • Fig. 3.16 Patient with xeroderma pigmentosum showing multiple ultraviolet-induced skin tumours
  • Molecular pathology of single-gene disorders
  • Fig. 3.17 Possible faults in protein biosynthesis.
  • Classification of mutations by their effects on function
  • Recommended nomenclature for sequence variants
  • Table 3.5 Examples of mutations causing cystic fibrosis
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • CHAPTER 4 DNA analysis
  • Key Topics
  • Introduction
  • Table 4.1 DNA-based detection methods used in diagnostic laboratories
  • Basic methods
  • Polymerase chain reaction
  • Fig. 4.1 Steps involved in amplification of a DNA segment using PCR. After several cycles, the amplified target short products predominate. dNTP: deoxynucleotide triphosphate.
  • Fig. 4.2 Exponential increase in product formed by PCR with increasing number of cycles on real-time PCR analysis. Fluorescence intensity is represented on the y-axis (as normalised intensity of the reporter dye ‘Rn’) and PCR cycle number is represented on the x-axis. The different exponential curves, from left to right, indicate PCRs carried out using serial tenfold dilutions of the same template DNA. With a more dilute template, the number of cycles required to generate the same product level increases. All reactions eventually level off at a plateau level where no further product can be generated, probably due to the depletion of reagents and the accumulation of inhibitory products. Image kindly provided by Alexander Fletcher, University of Glasgow.
  • Restriction digests
  • Fig. 4.3 Examples of restriction enzymes and their recognition sites.
  • Fig. 4.4 Diagram (a) and results (b) of PCR amplification of a portion of the β-globin (HBB) gene and digestion with MstII in a sickle-cell disease homozygote (lane 1), a sickle-cell heterozygote (lane 2) and two normal homozygotes (lanes 3 and 4). Lane 5 is a control containing amplified but undigested DNA. The vertical arrows in (a) indicate the restriction enzyme digestion sites. L5′ β and R5′ β represent the left and right PCR primers, respectively
  • Mutation detection
  • Pre-sequencing methods for mutation screening
  • Fig. 4.5 Pre-sequencing analysis of a patient’s DNA using dHPLC, following initial PCR and then heating and cooling to allow heteroduplex formation. In the lower fluorescence trace, the result (shown in red) can be seen for the PCR product for this region (exon 20 of the BRCA2 gene) at a detection temperature of 55°C. The middle trace (blue) represents the clearly abnormal result for that exon for a known mutation carrier (i.e. a positive control). The additional peak, to the left of the normal peak, is the result of the earlier release from a DNA-binding cartridge of the exon PCR product upon washing with a steadily increasing concentration of acetonitrile (with time shown on the x-axis). The additional peak represents the heteroduplex molecules, which elute (i.e. are released) earlier than the homoduplexes. In the upper trace (green), the additional peak is again clearly seen, indicating a possible sequence change in the sequence of this patient. This was an individual who was affected by familial breast cancer but for whom the BRCA2 gene had not yet been sequenced. The result, therefore, suggested that DNA sequencing should be performed on exon 20 of BRCA2 in that patient in order to determine whether or not a mutation was present. A single-nucleotide substitution was indeed subsequently found to be present. In practice, however, the changes in the output traces resulting from such mutations can be much less evident than that shown here.
  • Sanger (dideoxy) sequencing
  • Fig. 4.6 Difference between (a) ribonucleotides, (b) deoxyribonucleotide triphosphates (dNTPs) and (c) dideoxyribonucleotide triphosphates (ddNTPs). Ribonucleotides, present in RNA, possess a hydroxyl (-OH) group at both the 2′ and 3′ positions of the ribose. The dNTPs, present in DNA, have a 3′-OH group (although not a 2′-OH group). The ddNTPs, however, cause DNA chain termination because they possess a hydrogen (-H) instead of the-OH group at the 3′ position and therefore cannot react further. Courtesy of Maria Jackson and Leah Marks, University of Glasgow.
  • Fig. 4.7 Diagrammatic illustration of Sanger dideoxy sequencing. A forward or reverse primer is used, together with template DNA consisting of a product from a previous standard PCR. Many single-stranded products will be generated, each prematurely terminated when, by chance, a ddNTP (shown in colour, with a subscript ‘H’ indicating the 3′-H instead of 3′-OH group) is incorporated into the new molecule instead of the more abundant dNTP. The ddNTPs lack the 3′-OH group on the deoxyribose sugar that is necessary for further extension of the chain. After generation of the mixture of many single-stranded products, terminated at different positions with ddNTPs, the products are separated by electrophoresis through a gel (generally within a long capillary tube). As each of the four different ddNTPs is fluorescently labelled with a different fluorophore, the identity of the base at each position can be determined by detecting the colour or wavelength of fluorescence of each ddNTP as it passes through a detector near the end of the capillary. A computer interprets the emitted fluorescence signals and thus automatically determines the sequence of the DNA. The computer-determined sequence indicated with an arrow at the foot of the diagram shows only the portion of the DNA sequence into which fluorescent ddNTPs were incorporated. It therefore does not show the nucleotide sequence for the DNA that immediately precedes this region (i.e. GGACACT). Courtesy of Maria Jackson and Leah Marks, University of Glasgow.
  • Fig. 4.8 Electropherogram showing the DNA sequencing results for a patient affected by familial breast cancer who possesses a BRCA2 mutation. The result shows a single-nucleotide A to G substitution. This mutation (c.506A>G; p.Lys169Arg) can be seen to be heterozygous, as, at the substituted nucleotide (indicated by an arrow), there are two superimposed peaks, each resulting from the sequencing of one allele. The A is the nucleotide at that position in the wild-type or normal sequence, whereas the G represents the allele containing the mutation. The output shows the forward and reverse sequences, aligned so that the user can check that the sequence alteration has been detected by bidirectional sequencing to eliminate artefacts. A set of six traces is shown (a–f). The patient’s DNA sequence is indicated in the electropherogram trace that is second from the top (for sequencing using the forward primer; trace b) and second from the bottom (e; reverse direction), with the Genbank reference normal sequences being represented in the top and bottom traces (a and f, respectively) and a computerised prediction of mutation likelihood visible in the middle two traces (c and d).
  • Fig. 4.9 Electropherogram similar to that shown in Fig. 4.8, but showing the DNA sequencing results for a different, unrelated, patient, similarly affected by familial breast cancer. This patient, in contrast, possesses a deletion of 2 bp (indicated by an arrow), again in BRCA2. This mutation (c.4043_4044delGT; p.Cys1348Tyr FsX 3) can again be seen to be heterozygous. In this output, from the position of the deletion onwards, the sequence is difficult to read. This is because the sequence trace from the mutant allele is advanced by 2 nucleotides relative to the normal sequence, onto which it is superimposed. In the forward sequencing of the patient’s DNA (b), the traces appear to be disordered to the right of the start of the deletion, whereas in the reverse sequence (e), the disordered superimposed sequence is visible to the left of the deletion. The ‘FsX 3′ in the mutation nomenclature indicates that the frameshift in translation that results from the deletion of the 2 nucleotides causes protein truncation with a premature stop codon occurring just three codons downstream from the resulting amino acid substitution.
  • Massively parallel (‘next-generation’) sequencing
  • Screening for a set of recurrent mutations
  • Fig. 4.10 Results of a fluorescent ARMS test for 31 cystic fibrosis gene (CFTR) mutations. A commercial kit was used to analyse the commoner CFTR mutations in an affected patient. Two sets of fluorescent allele-specific primers were used. These were specific for individual mutants (the products being represented as blue peaks in a) or for individual normal sequences at those sites (shown in green, predominantly in b). The red traces represent PCR products from control primers included in both sets, designed to check that the test has worked. This patient is a compound heterozygote, with two different CFTR mutant alleles: ΔF508 (labelled as F508del) and W1282X.
  • Detection of deletions and duplications by DNA-based methods
  • Fig. 4.11 Results of MLPA for (a) the DNA of a male patient with an STS gene (X chromosome) deletion, revealed by the virtually absent blue (patient DNA) peaks for many PCR products relative to the red peaks (control DNA) and (b) a control patient. Fluorescence units are shown on the y-axis. Product lengths (in bp) are shown above the top x-axis and gene probe names are shown, compressed, below the bottom x-axis.
  • Fig. 4.12 Results from a multiplex ‘dosage’ PCR test for deletions/duplications in the Duchenne muscular dystrophy (DMD) gene. In this analysis, DNA from a female DMD obligate carrier was analysed using multiple sets of fluorescently labelled PCR primers that were designed to be individually specific for many different DMD exons. The results are shown in blue, with arbitrary units of fluorescence intensity shown on the y-axis and product length in base pairs on the x-axis. The red peaks represent the control PCR products (using DNA from a normal control individual) shown together with the blue peaks to allow the user to compare the relative heights of the patient and control peaks (reflecting the abundance of the corresponding PCR products). This permits the user to determine which exons, if any, appear to be present as just one copy in the case of a deletion (or three, in the case of a duplication) rather than two copies. In this case, the blue peaks for several exons (actually DMD exons 45–52) are reduced to approximately half the intensity of the red control peaks for those exons, indicating a probable intragenic deletion affecting these exons.
  • Other uses of microarrays in DNA analysis
  • Southern blotting
  • Fig. 4.13 (a) Smear of DNA fragments of various sizes after digestion of four DNA samples and gel electrophoresis (visualised under UV light after staining with ethidium bromide). (b) Diagram of the steps involved in involved in Southern blot analysis. (c) A Southern blot showing the results from two normal males (with EcoR1 restriction digest products of 5.2 kb in size in lanes 1 and 2) and an affected male (in lane 3). The DNA product from the affected male, of approximately 6.7 kb, is 1.5 kb larger than that from the unaffected males, as a result of an expansion of approximately 500 trinucleotide repeats.
  • Indirect mutant gene tracking
  • Table 4.2 DNA polymorphisms useful for indirect mutant gene tracking
  • Analysis of DNA length polymorphisms
  • Fig. 4.14 A (CA)n microsatellite length analysis (performed on an automated sequencer) following fluorescent PCR across an intragenic polymorphic marker. The traces for two siblings, affected by the same autosomal dominant condition known to be caused by this gene, are shown (a and b). Of the three main products (190, 208 and 210 bp, respectively), which result from different repeat lengths, the one that has been inherited by both affected siblings and therefore is most likely to represent the pathogenic allele of the gene, is the 190 bp product.
  • DNA fingerprinting
  • Fig. 4.15 DNA fingerprints. (a) From a rape victim, the semen specimen and three suspects. Which suspect which matches the specimen? (b) From a family where paternity was disputed: M, mother; C, child; F1 and F2 are the potential fathers. See questions 6 and 7 in Self-assessment. As mentioned in the text, DNA fingerprinting is now more commonly performed using microsatellite analysis by fluorescent PCR.
  • Quantitative fluorescent PCR
  • Analysis of single-nucleotide polymorphisms
  • SUMMARY
  • FURTHER READING
  • Self-assessment
  • CHAPTER 5 Chromosomes
  • Key Topics
  • Introduction
  • Chromosome structure
  • Fig. 5.1 A possible arrangement of DNA and its associated protein in the nucleosome, a chromatin fibre and a chromatid.
  • Chromosome analysis
  • Fig. 5.2 Normal human male karyotype (G-banding, 300 bands).
  • Fig. 5.3 Normal human female karyotype (G-banding, 800–1000 bands).
  • Fig. 5.4 Normal male karyotype (C-banding).
  • Fig. 5.5 Normal male karyotype (silver NOR stain). Note that not all acrocentrics are stained – this reflects NOR activity.
  • The normal human karyotype
  • Table 5.1 Symbols used for karyotype description
  • Fig. 5.6 Human idiogram (only the more prominent bands are numbered).
  • Flow karyotyping
  • Fig. 5.7 Flow karyotypes of a normal male and a normal female. The peaks correspond to individual chromosome pairs or groups of chromosomes as indicated.
  • Fig. 5.8 (a) Bivariate flow karyotype from a normal male. Chromosomes are sorted according to size and base-pair composition. Note that chromosomes 13, 15 and 22 resolve into their separate homologues. (b) Bivariate flow karyotype from a female patient (SR) with a 9:14 translocation with break points in 9q34 and 14q13. The derivative chromosomes sort near chromosome 3 and 21, respectively. (c) Comparison of the DNA content of chromosomes as measured by microdensitometry and flow cytometry reveals an excellent correlation (r2 = 0.999; y = 8.4822 + 94.781x). Note particularly that by both techniques chromosome 19 is smaller than 20 and chromosome 21 smaller than 22. The identity of these chromosomes was defined before DNA measurement was refined.
  • In situ hybridisation
  • DNA fibre FISH
  • Chromosome heteromorphisms
  • Size of Yq
  • Fig. 5.9 Yq polymorphisms.
  • Fig. 5.10 Fluorescent Y-chromatin.
  • Size of centromeric heterochromatin
  • Fig. 5.11 Chromosome 16 centromeric heterochromatin polymorphism (16qh+).
  • Fig. 5.12 Flow karyotype of 16qh+.
  • Satellite polymorphisms
  • Fig. 5.13 Tandem duplication involving a NOR on chromosome 15 (aceto-orcein staining).
  • Fragile sites
  • Fig. 5.14 Fragile site on chromosome 2 (at 2q13). (a) Site shown as a gap. (b, c) Site shown as chromatid break at gap. (d–f) Triradial chromosomes produced by chromatid breaks in previous division followed by non-disjunction of distal fragment. (g, h) Acentric fragments generated by chromatid breaks.
  • Copy number variation
  • Chromosomes in other species
  • Table 5.2 Numbers of chromosomes and protein-encoding genes in different species
  • Fig. 5.15 Normal gorilla karyotype.
  • Mitochondrial chromosomes
  • Mitosis
  • Fig. 5.16 Diagram of the cell cycle.
  • Fig. 5.17 Mitosis. Only two chromosome pairs are shown; the chromosomes from one parent are in outline, while those from the other are coloured.
  • Fig. 5.18 Sister chromatid exchanges (some arrowed).
  • Fig. 5.19 Chiasma formation in a somatic cell.
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • CHAPTER 6 Gametogenesis
  • Key Topics
  • Introduction
  • Meiosis
  • Fig. 6.1 Diagram of meiosis. Only two pairs of chromosomes are shown; chromosomes from one parent are in outline, while those from the other are coloured (cross-overs are indicated by arrows).
  • First meiotic division (reduction division)
  • Fig. 6.2 Human primary spermatocyte in leptotene.
  • Fig. 6.3 Zygotene.
  • Fig. 6.4 Homology of the banding pattern from meiotic (left) and mitotic chromosomes (chromosome 13 shown). Note the nucleolus arising from the short arm (top) of the bivalent.
  • Fig. 6.5 Pachytene.
  • Fig. 6.6 Early diakinesis. Note the multiple chiasmata (some indicated by arrows).
  • Fig. 6.7 Diagram of crossing-over.
  • Fig. 6.8 EM photomicrograph of the sex bivalent at pachytene showing the X chromosome (left) and the Y chromosome (right) attached by their pairing segments (top).
  • Second meiotic division
  • Fig. 6.9 Second meiotic metaphase showing a single condensed X chromosome.
  • Table 6.1 Comparison of mitosis and meiosis
  • Spermatogenesis
  • Fig. 6.10 Spermatogenesis.
  • Oogenesis
  • Fig. 6.11 Oogenesis.
  • Fertilisation
  • Table 6.2 Embryonic and fetal milestones
  • X-inactivation and dosage compensation
  • Fig. 6.12 Diagram of X-inactivation. Xm: maternal X chromosome; Xp: paternal X chromosome. Inactive X chromosomes are shaded.
  • Fig. 6.13 Barr body (arrow).
  • Fig. 6.14 Neutrophil drumstick (arrow).
  • Sex chromosome aberrations
  • 45,X (Turner syndrome)
  • Clinical features
  • Fig. 6.15 (a) Neonatal lymphoedema in Turner syndrome. (b) Redundant neck skin in Turner syndrome.
  • Genetic aspects
  • Recurrence risk
  • 47, XYY
  • Clinical features
  • Genetic aspects
  • 47, XXY (Klinefelter syndrome)
  • Clinical features
  • Genetic aspects
  • 47, XXX
  • Clinical features
  • Genetic aspects
  • Sex determination and differentiation
  • Genomic imprinting (parental imprinting)
  • Angelman syndrome
  • Clinical features
  • Fig. 6.16 Facial appearance in Angelman syndrome. Image kindly provided by Dr John Tolmie, Clinical Genetics Department, Yorkhill Hospitals, Glasgow, UK.
  • Genetic aspects
  • Prader–Willi syndrome
  • Clinical features
  • Fig. 6.17 (a) Prader–Willi phenotype. (b) Interstitial deletion of chromosome 15 (q11–q13).
  • Genetic aspects
  • Fig. 6.18 Microdeletion detection using specific FISH probes, with the deletions being identified by the absence of the locus-specific signal on one of the two chromosomes analysed in each case: (a) Hybridisation to a Miller-Dieker syndrome probe (PAFAH1B1, at 17p13.3) with a 17q-specific control probe reveals a deletion at the Miller-Dieker syndrome locus on one chromosome 17. (b) Hybridisation to a Williams syndrome probe (ELN, at 7q11.2) with a 7q-specific control probe shows a deletion at the Williams syndrome locus on one chromosome 7. (c) Hybridisation to a Prader-Willi/Angelman syndrome probe (SNRPN, at 15q11-q13) shows a deletion at the Prader-Willi/Angelman syndrome region on one chromosome 15. (d) Hybridisation to a DiGeorge/velocardiofacial syndrome probe (22q11.2) reveals a deletion at the 22q11.2 microdeletion syndrome region on one chromosome 22.
  • SUMMARY
  • FURTHER READING
  • Self-assessment
  • CHAPTER 7 Chromosome aberrations
  • Key Topics
  • Introduction
  • Numerical aberrations
  • Table 7.1 Examples of numerical chromosomal aberrations
  • Aneuploidy
  • Fig. 7.1 Non-disjunction of sex chromosomes at first meiosis, at second meiosis and at early cleavage.
  • Fig. 7.2 Detection of trisomy 18 using QF-PCR. Diagnosis of trisomy requires a clear trisomic pattern on a chromosome indicated by at least two informative markers. The chromosome number is indicated after the prefix ‘D’ in the marker label above each set of peaks (e.g. D21S11). The product length (in bp) is represented on the x-axis and by the first of three measurements given in each small box. The other two measurements represent the peak height and area, respectively. Two signals of approximately equal amplitude are detected for the markers on chromosomes 21 and 13 (which are disomic). For the polymorphic markers tested on chromosome 18, however, there are three signals (trisomic triallelic as for the marker D18S535) or, alternatively, two peaks with one peak being of approximately twice the size of the other (trisomic diallelic, as for the marker D18S391).
  • Polyploidy
  • Fig. 7.3 Triploidy detected at amniocentesis.
  • Structural aberrations
  • Table 7.2 Examples of structural chromosomal aberrations
  • Translocations
  • Reciprocal translocations
  • Fig. 7.4 (a) Reciprocal translocation between chromosomes 10 and 11. The normal chromosome is shown on the left for each pair. (b) Meiotic quadrivalent configuration in a 10;11 translocation. Chromosome 10 is shown at the top and chromosome 11 at the bottom. Normal chromosomes 10 and 11 are shown on the top right and lower left, respectively. (c) Meiotic quadrivalent at pachytene in a 10;11 translocation carrier (arrow). For simplicity, in the diagrammatic representation of the quadrivalent, whole chromosomes, rather than their individual chromatid components, are shown. (d) Electron micrograph of the synaptonemal complex of a 9;20 translocation observed at pachytene in a translocation carrier (stained with silver nitrate).
  • Fig. 7.5 (a) Reciprocal translocation between chromosomes 5 and 10. The normal chromosome is shown on the left for each pair. (b) Meiotic ring quadrivalent (R4) for a balanced 5; 10 reciprocal translocation at first meiosis. (c) Meiotic chain quadrivalent (C4, arrow) at diakinesis. (d) Three types of 2 : 2 segregation for a balanced 5; 10 reciprocal translocation at first meiosis. Note that the four types of 3 : 1 segregation are not shown. Except in specific translocations, such as an 11;22 translocation, the unbalanced offspring resulting from a 3 : 1 segregation would not be viable and a miscarriage would result from the gross chromosomal imbalance. For simplicity, the two individual chromatids that would be present are not shown in the first and final stages of this figure and are represented instead by a single chromosome.
  • Fig. 7.6 Maternal reciprocal translocation between chromosomes 11 and 22 with 3 : 1 segregation to produce partial duplication of chromosomes 11 and 22 in a daughter with significant learning disability. In the 3 : 1 segregation, the daughter inherited the mother’s der(22;11) in addition to the mother’s normal chromosome 11 and normal chromosome 22.
  • Robertsonian (centric fusion) translocations
  • Fig. 7.7 Accidental recombination between homologous regions of non-homologous chromosomes during meiosis as a cause of dicentric centric fusion chromosomes.
  • Fig. 7.8 Robertsonian translocation of chromosomes 14 and 21.
  • Fig. 7.9 Meiotic trivalent for a t(13; 14) Robertsonian translocation (arrow).
  • Fig. 7.10 Segregation of a Robertsonian translocation at first meiosis. For simplicity, as in Figs 7.4 and 7.5, whole chromosomes rather than their individual component chromatids are shown.
  • Insertional translocations
  • Fig. 7.11 Insertional translocation showing interstitial deletion of band 1q31 and insertion into band 5q13 (arrows).
  • Deletions and ring chromosomes
  • Fig. 7.12 (a) Ring chromosomes, dicentrics and acentric fragments following exposure to irradiation. (b) Double-ring chromosome 13.
  • Duplications
  • Fig. 7.13 Results of unequal crossing-over.
  • Inversions
  • Fig. 7.14 (a) Two examples of paracentric inversions of chromosome 12. (b) Pericentric inversion of chromosome 9; this inversion is present in 1% of the normal population (this patient coincidentally has trisomy 21).
  • Fig. 7.15 Electron micrograph of the synaptonemal complex of a 46,XY,inv(2)(p13;q25) carrier. Homologous pairing has been achieved by one homologue forming an inversion loop.
  • Fig. 7.16 Large pericentric inversion of chromosome 7. The normal chromosome in each case os shown on the left. (a) Parent with balanced inversion. (b) Abnormal child with duplication (7q32-qter) and deficiency (7p22-pter) resulting from a cross-over within the paternal inversion.
  • Fig. 7.17 The results of crossing-over at meiosis (a, b) within and (c) outside the pericentric inversion of chromosome 7, as shown in Fig. 7.16. A is the normal chromosome 7 and D has the pericentric inversion. In (a) and (b), two types of abnormal recombinant chromosome are formed (B and C, each with a duplication deficiency). In (c), crossing-over outside the inversion produces no abnormal recombinant.
  • Isochromosomes
  • Fig. 7.18 (a) Dicentric isochromosome for the long arm of the X. Staining by G-banding (left pair) and C-banding (right pair). The dicentric is the chromosome on the right in each pair. (b) Dicentric isochromosome for the short arm of chromosome 9 in a patient with the features of trisomy 9p syndrome. Only one centromere (the top one) is functional.
  • Marker chromosomes
  • Cytogenetic and molecular methods for the detection of chromosomal aberrations
  • Cytogenetic methods
  • Fluorescence in situ hybridisation
  • Fig. 7.19 Use of multicolour FISH probes to determine chromosome copy number in interphase nuclei. (a) Lymphocyte metaphase and interphase nuclei showing centromeric probes for the X chromosome (lilac), Y chromosome (yellow) and chromosome 18 (dark blue); a YAC clone marks chromosome 13q (green) and two overlapping cosmid clones mark chromosome 21 (red). (b) Uncultured amniotic fluid cell nucleus from a female fetus hybridized with the above probes, revealing a normal number of each chromosome. (c) As in (b), from a normal male fetus. (d) As in (b), from a male fetus with trisomy 21 (Down syndrome). From Divane et al., Prenatal Diagnosis 1994; 14: 1061–69).
  • Fig. 7.20 Derivative chromosome 13 resulting from a balanced reciprocal 8;13 translocation identified in a pair of monozygotic twins affected by the CHARGE association. Mapping of the chromosome 8 breakpoint was undertaken using a series of FISH probes, leading to the identification of the causative CHD7 gene. The relative positions of the chromosome 8-specific FISH probes are indicated. Probe RP11 33111 spanned the breakpoint on chromosome 8. Clones to the right of the long vertical line mapped to the der(13) and normal 8. Probe 10.1 kb (which spanned exons 4 and 5) localised to both the normal and the derivative chromosome 8, while probe 9.1 kb (which spanned exons 6 and 7) localised to both derivative chromosomes 8 and 13. Reproduced from Journal of Medical Genetics, Johnson et al., 43, 280–4. © 2006 with permission from BMJ Publishing Group Ltd.
  • DNA-based methods
  • Quantitative fluorescent PCR
  • Fig. 7.21 (a) QF-PCR result for a pregnancy affected by trisomy 21. The graph shows either trisomic diallelic (two peaks with a 2 : 1 size ratio) or triallelic patterns for the microsatellite markers on chromosome 21, but normal diallelic peaks of approximately equal sizes for chromosomes 18 and 13. An uninformative homozygous marker (producing a single unhelpful peak) on chromosome 18 and also for chromosome 13 is also visible, resulting from a pair of alleles that possess the same number of repeats. (b) QF-PCR result for a pregnancy affected by trisomy 13.
  • Multiple ligation-dependent probe amplification
  • Fig. 7.22 (a) MLPA result for a patient affected by Williams syndrome. The blood DNA MLPA results (top) are shown together with a chart showing the peak ratios for each probe (bottom). The patient possesses a microdeletion on one chromosome 7, as can be seen from the reduced size of the blue peaks relative to the red control peaks (with a ratio of approximately 0.5 instead of 1.0) for the six DNA probe sequences that are located within the deleted region. The probes are displayed by the analysis software in order of sequence length rather than according to their order along the chromosome. The MLPA kit was obtained from MRC-Holland. (b) MLPA results for the Williams syndrome region on chromosome 7, using DNA from a normal control individual.
  • Array comparative genomic hybridisation
  • Figs. 7.23 (a–c) Images showing an aCGH slide (‘CytoChip’ from BlueGnome Ltd) at increasing magnification. The slide shown uses BAC microarrays to permit investigation of genomic copy number at a higher resolution (approximately 500 kb on average) than would be possible by standard karyotyping (approximately 4 Mb). The spots represent different known genomic loci. Intensely red or green signals indicate an excess of patient relative to control DNA or vice versa. The presence of two identical hybridisation areas on each slide (the upper and lower grids in (a)) permit the use of a ‘dye-swap’ technique, in which the fluorescent labelling of patient and control DNA samples are reversed for one of the hybridisation areas, in order to allow confirmation of the results. Even higher resolution (e.g. 11–14 kb in clinically important genomic regions) can be obtained using oligo-array CGH (greater numbers of spots are present on the slide, each spot containing an oligonucleotide, rather than a BAC clone).
  • Fig. 7.24 aCGH results of chromosome 17 in a patient with mild hereditary motor and sensory neuropathy (HMSN). The altered ratio of fluorescence, of patient DNA (Ch1) compared with control (Ch2) is clearly indicated (green line adjacent to the chromosome idiogram) at the region on 17p that is affected by a microduplication. The abnormality is confirmed on the superimposed dye-swap profile showing inverted ratios (red trace). It is known that duplication of the gene encoding peripheral myelin protein-22 (PMP22) in this region (17p11.2) is a common cause of HMSN type 1A (also known as Charcot–Marie–Tooth disease type 1A). When the diagnosis is suspected clinically, the duplications at this site are more usually detected by MLPA.
  • Fig. 7.25 Interphase FISH image showing the presence of three signals instead of the normal two, using a probe hybridising to the region on chromosome 17p11.2 containing the PMP22 gene. This confirms the presence of the microduplication at this region that was indicated on aCGH (Fig. 7.23). Such duplications would not be clearly visible by FISH on a metaphase spread due to the proximity of the two signals on the same chromosome.
  • Fig. 7.26 aCGH analysis of a patient with a t(4;20) unbalanced translocation. (a) Chart showing ratio of patient to control DNA across the genome, using aCGH with BAC clones spaced at a median of 565 kb generally, at 250 kb at the subtelomeric regions and at 100 kb at 90 specific known disease loci. Regions of clinically significant abnormality were detected on chromosomes 4 and 20, resulting from the unbalanced translocation. (b, c) Individual aCGH chromosome profiles showing a deletion on the long arm of chromosome 4 and a duplication on the short arm of chromosome 20 in the patient with the unbalanced t(4;20) represented in (a).
  • Identification of the chromosomal origin of complex structural rearrangements
  • Fig. 7.27 Identification of chromosomes 18 and the X in metaphase and interphase using FISH. Alphoid centromeric repeat probes were detected with FITC (chromosome 18; green) and Texas red (X chromosome; bright red), counterstained with propidium iodide (dark red). Karyotype 46, XY.
  • Fig. 7.28 Examples of chromosome-specific painting. (a) A small reciprocal translocation involving the distal ends of the long arms of chromosome of chromosomes 1 and 2 is difficult to distinguish by G-banding. (b) The same translocation revealed by hybridization with chromosome 1-specific paint (red) and chromosome 2-specific paint (green). (c) The result following chromosome painting of a male metaphase with a Y chromosome-specific paint (green) and an X chromosome-specific paint (red). Regions of Y homology on the X chromosome (the tip of Xp and the proximal third of Xq) or of X homology on the Y chromosome (the tip of Yp) appear yellow due to the combined red and green fluorescence. Note that the PAR2 region at the tip of Xq (mentioned in Chapter 6) is too small to produce a signal. Also, no green signal is visible in the heterochromatic region of Yq because the DNA repeats are suppressed by the hybridisation method that was used. (d) Example of three-colour forward chromosome painting: chromosome 1 (red), chromosome 2 (green) and chromosome 6 (yellow).
  • Fig. 7.29 Reverse painting in the analysis of a 46,XX, t(2;17)(q31;q25) translocation. (a) G-banded preparation showing chromosomes 2 and 17 and their derivatives from a balanced translocation carrier. (b) Flow karyotype showing the positions of the two derivative chromosomes from which paint probes were prepared following chromosome sorting and amplification. (c) The der 2 probe (green) and the der 17 probe (red) hybridized to a normal male metaphase to confirm the origin and breakpoints of the translocation. (d) The same der 2 and der 17 paints hybridized to a metaphase from the balanced translocation carrier.
  • Fig. 7.30 Multicolour FISH using a paint probe composed of a combination of all 24 chromosome-specific probes, each labelled with a different combination of five fluorochromes and analysed by spectral imaging. Reprinted with permission from Schröck et al., Science, 1996; 273:494–497. ©1996 American Association for the Advancement of Science.
  • Other aberrations
  • Mosaic
  • Chimaera
  • Uniparental disomy and isodisomy
  • Fig. 7.31 Diagram of the mechanism of origin of uniparental disomy and isodisomy.
  • SUMMARY
  • FURTHER READING
  • Self-assessment
  • Fig. 7.32 See Question 7.
  • CHAPTER 8 Typical Mendelian inheritance
  • Key Topics
  • Introduction
  • Fig. 8.1 Symbols used in pedigree construction.
  • Introduction to autosomal single-gene inheritance
  • Autosomal dominant inheritance
  • Fig. 8.2 Tendon xanthomata in familial hypercholesterolaemia.
  • Fig. 8.3 Pedigree of a family with familial hypercholesterolaemia. The patient in Fig. 8.2 is indicated by an arrow.
  • Fig. 8.4 Diagram of autosomal dominant inheritance.
  • Table 8.1 Autosomal dominant diseases
  • Autosomal recessive inheritance
  • Fig. 8.5 Sickle-shaped red cells in a sickle haemoglobin (HbS) homozygote.
  • Fig. 8.6 Haemoglobin electrophoresis at alkaline pH to demonstrate individuals who are homozygous for HbS, heterozygous (HbS/HbA) or homozygous normal (HbA/HbA).
  • Fig. 8.7 Pedigree of a family with children affected with sickle-cell disease.
  • Fig. 8.8 Diagram of autosomal recessive inheritance.
  • Fig. 8.9 Relative proportions of affected to unaffected offspring when both parents are carriers for an autosomal recessive trait and have two children.
  • Table 8.2 Proportions of genes in common in different relatives
  • Table 8.3 Ethnic associations with autosomal recessive diseases
  • Table 8.4 Autosomal recessive diseases
  • Summary of autosomal inheritance
  • Table 8.5 Typical features of autosomal dominant and recessive modes of inheritance
  • Introduction to sex-linked inheritance
  • Table 8.6 Comparison of typical features of autosomal dominant with male sex limitation inheritance and X-linked recessive and dominant inheritance
  • X-linked recessive inheritance
  • Fig. 8.10 Pedigree of a family with severe X-linked muscular dystrophy (DMD).
  • Fig. 8.11 Expected proportions of offspring for a female X-linked recessive heterozygote.
  • Fig. 8.12 Distribution of serum CK levels in normal females and obligate carriers for DMD. Courtesy of Douglas Wilcox, University of Glasgow.
  • Fig. 8.13 Pedigree of a family with only one child affected by DMD.
  • Fig. 8.14 An X–autosome translocation in a female with DMD t(X;7)(p21;q32).
  • Table 8.7 Human X-linked recessive traits
  • Fig. 8.15 Diagram of the expected proportions of offspring for an affected male with an X-linked recessive trait.
  • X-linked dominant inheritance
  • Fig. 8.16 Pedigree of a family with vitamin D-resistant rickets.
  • Table 8.8 Examples of human X-linked dominant traits
  • Y-linked inheritance (holandric inheritance)
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • CHAPTER 9 Atypical Mendelian inheritance
  • Key Topics
  • Introduction
  • Genetic anticipation
  • Huntington disease
  • Fig. 9.1 Illustrative pedigree of a family with Huntington disease. The age of onset of symptoms is shown above the number of CAG repeats for each affected individual. The age of onset decreases as the number of repeats increases, in successive generations (i.e. typical genetic anticipation).
  • Fragile X syndrome
  • Fig. 9.2 Fragile site at Xq27.3. (a) Normal X chromosome (G-banding). (b) Fragile site visible as a ‘gap’.
  • Spinocerebellar ataxia type I
  • Myotonic dystrophy
  • Pseudoautosomal inheritance
  • Autosomal dominant inheritance with sex limitation
  • Pseudodominant inheritance
  • Fig. 9.3 Pedigree illustrating Gilbert syndrome inheritance. The occurrence of the condition in two generations of the family, together with apparent male-to-male transmission, might suggest autosomal dominant inheritance. The condition is now known, however, to be inherited in an autosomal recessive manner but with such a high carrier frequency that affected individuals may be found in more than one generation. Mutation analysis, if performed, would reveal the presence of two UGT1A1 mutant alleles in II: 2, II: 4, III: 3 and III: 4 as well as a single mutant UGT1A1 allele in individual II: 5 (a carrier).
  • X-linked dominant inheritance with male lethality
  • Mosaicism
  • Fig. 9.4 Pedigree illustrating a family with tuberous sclerosis (TS). In this family, a second affected child has been born to the clinically unaffected mother, I:2. Mutation analysis of blood DNA may reveal a TS gene mutation in II: 1 but not in either of his parents. The same mutation, however, would be present in the blood DNA of II: 3, as a result of gonadal mosaicism in I:2.
  • Modifier genes and digenic inheritance
  • Modifier genes
  • Digenic inheritance
  • Uniparental disomy
  • Fig. 9.5 Diagram showing how paternal or maternal UPD can arise by the inheritance of both members of a chromosome pair from either the father or the mother, respectively. Uniparental heterodisomy refers to the inheritance of both chromosomes from the parent, whereas uniparental isodisomy refers to the inheritance of two identical copies of just one parental chromosome.
  • Table 9.1 Examples of syndromes that may result from UPD
  • Imprinting disorders
  • Fig. 9.6 Pedigree of the family reported by Schulze et al. (2001) in which the individual II: 2 inherited a deletion at 15q11-q13 from her father and thus developed Prader–Willi syndrome (PWS). The daughter of II: 2 subsequently inherited the deletion from her and thus was affected by Angelman syndrome (AS).
  • SUMMARY
  • FURTHER READING
  • WEBSITE
  • Self-assessment
  • CHAPTER 10 Non-Mendelian inheritance
  • Key Topics
  • Introduction
  • Multifactorial disorders
  • Twin concordance studies
  • Fig. 10.1 Diagnosis of zygosity from the appearance of the placental membranes.
  • Determination of concordance
  • Results of twin studies
  • Table 10.1 Concordance rates in twins if a particular inheritance pattern is followed exclusively
  • Table 10.2 Degree of similarity of twins for continuous traits
  • Table 10.3 Twin concordance for some discontinuous traits
  • Family correlation studies
  • Table 10.4 Proportion of genes shared by relatives
  • Table 10.5 Family correlations for some continuous traits
  • Table 10.6 Frequency of discontinuous traits for differing degrees of relationship
  • Continuous multifactorial traits
  • Table 10.7 Examples of human continuous multifactorial traits
  • Fig. 10.2 Gaussian distribution of height in English adult males.
  • Discontinuous multifactorial traits
  • Table 10.8 Discontinuous human multifactorial traits
  • Fig. 10.3 Expected distribution of colour in offspring if the trait is due to (a) a single locus with two alleles, (b) two loci each with two alleles and (c) three loci each with two alleles. Note the approach towards a Gaussian distribution.
  • Fig. 10.4 Cleft lip and palate.
  • Fig. 10.5 General population liability curve for cleft lip and palate.
  • Fig. 10.6 Displaced liability curve in first-degree relatives of a proband with cleft lip and palate.
  • Table 10.9 Multifactorial conditions with an unequal sex ratio
  • Table 10.10 Pyloric stenosis frequency in relatives
  • Analysis of the genetic determinants of multifactorial traits
  • Somatic cell genetic disorders
  • Mitochondrial disorders
  • Fig. 10.7 Pedigree from a family with Leber hereditary optic neuropathy showing mutation carriers, not all of whom were symptomatic.
  • Table 10.11 Examples of conditions with mitochondrial inheritance
  • SUMMARY
  • FURTHER READING
  • Self-assessment
  • CHAPTER 11 Medical genetics in populations
  • Key Topics
  • Introduction
  • Selection for single-gene disorders
  • Fig. 11.1 Effect of selection on the frequency of a condition within a population.
  • Founder effect and genetic drift for single-gene disorders
  • Table 11.1 Examples of genetic isolates with relatively high frequencies of certain single-gene disorders
  • Altered mutation rate for single-gene disorders
  • Table 11.2 Equations for prediction of birth frequency of single-gene disorders
  • Linkage analysis and the International HapMap Project
  • Fig. 11.2 The identification of various haplotypes and the so-called ‘tag’ SNPs that are selected to represent them uniquely, by the International HapMap Project. In (a), the individual SNPs are shown in colour to differentiate them from the surrounding non-variant chromosomal DNA sequences. These SNPs, together with other surrounding SNPs, can then be grouped and examined as haplotypes, shown in (b). From these haplotypes, individual tag SNPs (c) can then be chosen that can be used to represent the individual haplotypes, their presence or absence thus predicting the surrounding SNP genotypes. Redrawn, with modifications, from International HapMap Consortium (2003) Nature 426:789–796.
  • Fig. 11.3 Computer-generated linkage disequilibrium (LD) plot for a 100kb region of chromosome 6 that contains the HLA-A major histocompatibility gene from the HapMap database (at http://www.hapmap.org). An area of strong linkage disequilibrium can be seen as a dense red triangle in the lower panel that corresponds to a region of approximately 14 kb of chromosome 6, located about 30 Mb from the end of the short arm. International HapMap Consortium (2003) Nature 426:789–796.
  • Human population evolution and migration
  • Fig. 11.4 Human migration paths deduced from the analysis of variation at individual Y chromosomal DNA markers in a large number of living individuals. Each marker is numbered (e.g. M343) and can be used to track individual male lineages. The approximate ages of the lineages and where they first appeared are represented by different colours. Reprinted from Stix, 2008 (see Further Reading), with permission from Nature Publishing Group.
  • Fig. 11.5 The Out-of-Africa theory has now largely replaced the Multiregional theory as a model of the way in which the world was colonised by modern humans. The Out-of-Africa theory proposes that Homo sapiens originated in Africa and then, beginning around 60,000 years ago, migrated out of Africa, replacing earlier hominids such as Homo erectus, which had colonised other parts of the world from 1.8 million years ago. Reprinted from Stix, 2008 (see Further Reading), with permission from Nature Publishing Group.
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • Part 2 Clinical Applications
  • CHAPTER 12 Genetic assessment, genetic counselling and reproductive options
  • Key Topics
  • Introduction
  • Communication of advice
  • History and pedigree construction
  • Fig. 12.1 Symbols used in pedigree construction.
  • Fig. 12.2 Example of a family pedigree.
  • Clinical examination
  • Table 12.1 Descriptive terms used in dysmorphology
  • Fig. 12.3 Facial landmarks.
  • Table 12.2 Measurements that may be diagnostically useful
  • Fig. 12.4. A single transverse palmar crease. Courtesy of Margo Whiteford, Yorkhill Hospital, Glasgow.
  • Confirmation of diagnosis
  • Table 12.3 Diagnosis of genetic disease
  • Table 12.4 Indications for chromosomal or DNA analysis. Such analyses may also subsequently be carried out as appropriate in the proband’s relatives to identify those at risk. This could include the identification of carriers of, for instance, a balanced chromosome rearrangement or a colon cancer-predisposing gene mutation
  • Counselling
  • Table 12.5 General population risks
  • Table 12.6 Common misconceptions about heredity
  • Fig. 12.5 Reproductive options available following diagnosis of a genetically inherited condition.
  • Follow-up
  • Special points in counselling
  • Table 12.7 Pitfalls and problems in genetic counselling
  • Single-g ene disorders
  • Multifactorial disorders
  • Consanguinity
  • Prenatal diagnosis
  • Table 12.8 Identification of at-risk pregnancies
  • Table 12.9 Techniques for prenatal diagnosis
  • Amniocentesis
  • Table 12.10 Tests on amniotic fluid cells and supernatant
  • Fetal sexing
  • Fig. 12.6 Sexing amniotic fluid cells by demonstration of the Barr body. In this case, two Barr bodies are present (arrows), indicating the presence of three X chromosomes. Full chromosome analysis showed 47, XXX.
  • Fetal karyotyping
  • Fig. 12.7 A karyotype from amniotic fluid demonstrating an extra copy of chromosome 20, which was present in 25% of cells from several cultures (true mosaicism).
  • Fig. 12.8 Results of FISH undertaken on uncultured amniocytes: (a) The result after using a commercial 22q11.2-specific probe (designed to detect microdeletions associated with velocardiofacial syndrome), in red, in combination with a 22q-specific control probe in green. The image shows an abnormal signal pattern (one red and two green signals), as observed in the majority of cells scored, suggestive of the presence of the 22q11.2 microdeletion on one chromosome 22. (b) The result following the use of a commercial probe combination consisting of an X centromere-specific probe labelled with a green fluorophore and a Y centromere-specific probe labelled in red. Two nuclei exhibit two green signals and one red signal, while one has one green and one red, suggesting that the fetus is an XXY/XY mosaic. Courtesy of Norma Morrison, Yorkhill Hospital, Glasgow.
  • Fetal enzyme assay
  • Table 12.11 Examples of prenatally diagnosable inborn errors of metabolism (when suspected)
  • Amniotic fluid biochemistry
  • Fetal DNA diagnosis of single-gene disorders
  • Table 12.12 Current major indications for fetal DNA diagnosis of single-gene disorders
  • Risks of amniocentesis
  • Chorionic villus sampling
  • Fig. 12.9 (a) Normal fetus at 10 weeks of gestation. (b) Anembryonic sac at 10 weeks of gestation.
  • Cordocentesis, fetal skin biopsy and fetal liver biopsy
  • Table 12.13 Possible indications for fetal blood sampling
  • Ultrasonography
  • Table 12.14 Examples of congenital malformations that can usually be diagnosed by ultrasound
  • Fetal cells in the maternal circulation
  • Free fetal DNA and RNA detection
  • Preimplantation genetic diagnosis
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • CHAPTER 13 Family history of cancer
  • Key Topics
  • Introduction
  • General principles
  • Tumour suppressor genes
  • Fig. 13.1 A simplified representation of the roles of RB and p53. These include cell-cycle arrest via transcriptional activation by p53 of the p21 protein. The p21 protein then inhibits the phosphorylation of RB by cyclin/CDK complexes and thus causes loss of transcriptional activation by E2F/DP regulatory proteins. This occurs because, when RB is hypophosphorylated, it can bind to (and thus inhibit) E2F transcriptional regulatory proteins. Another important effect of p53 is programmed cell death (apoptosis), which occurs via the p53-triggered release of cytochrome c from mitochondria and the subsequent activation of a series of proteases known as caspases.
  • Fig. 13.2 (a) Sporadic and (b) inherited retinoblastoma. Copies of chromosome 13 are shown with either a normal (N) or an abnormal (A) gene.
  • Fig. 13.3 Mechanisms of loss of a second retinoblastoma allele. N, Normal gene; A, mutant gene.
  • Fig. 13.4 LOH for a DNA polymorphic marker with two alleles (arrows). Complete loss of one allele in patients 1 and 2, partial loss in patient 3 and no loss indicating another mechanism in patient 4. S, Somatic tissue or blood; T, tumour tissue.
  • Table 13.1 Examples of genetic conditions predisposing to tumours, relatively commonly seen in genetics clinics
  • Table 13.2 Genetic conditions predisposing to tumours, less commonly seen in genetics clinics
  • Fig. 13.5 Demonstration, using fluorescent PCR amplification of an intragenic polymorphic marker sequence, of partial loss of one allele of the NF1 gene in the DNA of an unusual gastric tumour arising in an individual with an inherited NF1 gene mutation. The tumour DNA PCR products are represented in red while the blood DNA PCR products are shown in blue. The results are consistent with reduced dosage of one allele (or allelic imbalance) in the tumour DNA, representing almost complete LOH.
  • Fig. 13.6 Previously proposed model of stages in progression from normal colonic epithelium to metastatic cancer. More recent evidence suggests that this model is likely to be most applicable to only a minority of colonic carcinomas and would not be applicable to tumours arising in hereditary non-polyposis colon cancer (HNPCC).
  • Genes involved in DNA repair mechanisms
  • Oncogenes
  • Fig. 13.7 A metaphase spread showing double minutes (some arrowed).
  • Fig. 13.8 Philadelphia chromosome (Ph′) resulting from a reciprocal translocation between chromosomes 9 and 22, specifically t(9;22) (q34;q11).
  • Other cancer-related genes
  • Genetic counselling aspects of cancer
  • Common familial cancer predisposition syndromes
  • Breast and ovarian cancer
  • The BRCA 1 and BRCA 2 genes
  • The BRCA 1 and BRCA 2 proteins
  • Fig. 13.9 Diagram showing selected interactions and functional regions of the BRCA1 protein. The protein is large, comprising 1863 amino acids, and is believed to participate in the repair of double-strand breaks in DNA via its interaction with RAD50, NBS1 and MRE11. Several additional interactions have been described for the protein, a number of which are indicated. The interaction with BRCA2 may occur directly, through the BRCA1 C-terminal (BRCT) domains and/or via RAD51. Following double-strand DNA breaks, ATM protein phosphorylates BRCA1 at its clusters of serines and threonines within the SQ cluster domains.
  • Mutation detection
  • Cancer prevention and early detection
  • Colorectal cancer
  • Hereditary non-polyposis colon cancer (Lynch syndrome)
  • Familial adenomatous polyposis (polyposis coli, Gardner syndrome)
  • Fig. 13.10 CHRPE in FAP. Reproduced from Tobias, ES, and Connor, JM, 2008. Genetic counselling for childhood tumors and inherited cancer predisposing syndromes. In The Surgery of Childhood Tumors, 2nd edn, pp. 33–48. Edited by Carachi R, Grosfeld JL and Azmy AF. Springer. With kind permission of Springer Science + Business Media.
  • MUTYH-associated (MYH-associated) polyposis
  • Genes and mutations in hereditary colorectal cancer
  • Fig. 13.11 Human mismatch repair system. Repair of mismatched bases following DNA replication involves several proteins and steps. The mismatch is initially bound by the heterodimer composed of MSH2 and MSH6. This is followed by binding of MLH1 and PMS2 to form a complex that then triggers an exonuclease to digest the newly synthesised strand, allowing DNA polymerase to resynthesise the strand with the correct base sequence.
  • Fig. 13.12 Simplified illustration of the physiological role of APC protein in the WNT pathway. The APC protein, together with AXIN and GSK3, cooperate in preventing overaccumulation of the transcriptional cofactor β-catenin by promoting its phosphorylation, ubiquitination (molecular marking of the protein for subsequent breakdown) and degradation in the proteasome. Physiological WNT signaling or mutational APC (or AXIN) inactivation therefore both lead to inhibition of the phosphorylation of β-catenin, and thus result in increased levels of this transcriptional coactivator. β-Catenin is also bound by the cell–cell adhesion protein, E-cadherin. The inactivation of E-cadherin (as occurs in hereditary diffuse gastric cancer) can therefore lead not only to reduced cell–cell adhesion but also to an increase in free β-catenin.
  • Prevention and early detection
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • Fig. 13.13 A 27-year-old woman attends the genetics clinic seeking advice. She is the sister of a woman who developed breast cancer at the age of 35. Their mother developed breast cancer aged 36 and again, in the other breast, aged 42. Their maternal aunt was diagnosed with ovarian cancer at the age of 42 and their maternal grandmother died of breast cancer at the age of 47. See Questions 4 and 5 in the Self-assessment.
  • Fig. 13.14 A 30-year-old man is found to have four adenomatous polyps in the sigmoid colon at colonoscopy. He mentions that his father died at the age of 45 with colon cancer (after having been diagnosed at 44), his paternal aunt was treated for rectal cancer at 45 and his paternal grandfather was treated for colon cancer at 50. He asks about the likely underlying cause of the cancers occurring in the family. See Q7 and Q8 in Self-assessment.
  • CHAPTER 14 Family history of common adult-onset disorder
  • Key Topics
  • Introduction
  • General principles
  • Diabetes mellitus: common and monogenic forms
  • Fig. 14.1 Various loci associated with susceptibility to type 2 diabetes. The relatively small (estimated) effects (calculated as odds ratios) are indicated on the x-axis. Genes shown in blue were identified by genome-wide association studies, whereas those shown in red were found by analysing pre-selected genes. Modified from Prokopenko et al., 2008 Trends Genet. 24(12):613–22, with permission from Elsevier; see Further reading.
  • Fig. 14.2 Model for the role of environmental and genetic factors in the development of type 2 diabetes.* KCNJ11 and also TCF7L2, are genes whose variants are believed to result in a reduction in insulin secretion by causing diminished islet β-cell function. Modified from Prokopenko et al., 2008 Trends Genet. 24(12):613–22, with permission from Elsevier; see Further reading.
  • Genes of major effect and associated conditions
  • Maturity-onset diabetes of the young
  • Mitochondrial diabetes
  • Severe insulin resistance syndromes
  • Dementia: Alzheimer disease, Huntington disease, prion diseases and other causes
  • Alzheimer disease
  • Genetic predisposition
  • Fig. 14.3 Amino acid sequence encoded by exons 16 and 17 of APP. Red and green amino acids represent those for which there are reported pathogenic and non-pathogenic missense substitutions, respectively. Pathogenic mutations are frequently found close to secretase cleavage sites. Typical Alzheimer disease phenotypes result from mutations that affect the beta and gamma secretase cleavage sites, with the release of amyloid β42 peptide. Modified from Dermaut et al., 2005 Trends Genet. 21:664–72, with permission from Elsevier; see Further Reading.
  • Other forms of dementia
  • Frontotemporal dementia with parkinsonism-17
  • Huntington disease
  • Fig. 14.4 Clinical effects of different numbers of CAG repeats within the Huntington disease (HTT) gene coding region.
  • Prion diseases
  • SUMMARY
  • FURTHER READING
  • Self-assessment
  • Fig. 14.5 This pedigree shows a family in which several members have been known to be affected by type 2 diabetes from the ages of diagnosis (Dx) shown. Graham (individual III:1) has been feeling unusually tired over the past 4 months and is eventually tested for diabetes. Unfortunately, Graham is also confirmed as having diabetes, at the age of 21, and the family are referred to the genetics department for further advice. See questions 1–3 in Self-assessment.
  • Fig. 14.6 Billy, individual IV: 1 in this family, aged 28, mentions to his family doctor that he is worried that he may develop dementia at an early age. Billy met his grandfather (II:6) recently in a nursing home and was dismayed to discover that his grandfather had forgotten his name and that he had, in fact, developed Alzheimer disease, like Billy’s grandfather’s late elder sister (II:2). These two individuals had been diagnosed with the condition at the ages of 78 and 74. Billy was sufficiently concerned about the possible implications for himself that the family doctor decided to refer him to see a geneticist for advice. See Question 4 in Self-assessment.
  • CHAPTER 15 Strong family history – typical Mendelian disease
  • Key Topics
  • Introduction
  • Cystic fibrosis
  • The gene and its mutations
  • Genetic counselling
  • Testing
  • Fig. 15.1 Linda (III:2 in the pedigree), the 20-year-old apparently healthy elder sister of a boy affected by cystic fibrosis, comes to the genetics clinic. She hopes to have a child and seeks advice regarding the risks to her future child. Her partner (III:1) is healthy, not related to her and has no family history of genetic conditions himself. See text and Self-assessment questions 1–3 for a discussion of the risks.
  • Table 15.1 Calculation of CF carrier risk using Bayes’ theorem in an individual with a prior carrier risk of 1 in 20, who then tests negative on a CF mutation screening test that detects 90% of CFTR mutant alleles
  • Fig. 15.2 Autosomal recessive trait in a family, with carrier risks indicated for each individual. f, General population carrier frequency.
  • Other general points
  • Duchenne and Becker muscular dystrophies
  • The gene and its mutations
  • Fig. 15.3 The DMD gene, the largest gene found in nature to date, spanning approximately 2.2 Mb of genomic DNA on the short arm of the X chromosome. In this University of California, Santa Cruz (UCSC) genome browser window (see Chapter 19 for further details; Kent et al. (2002) The human genome browser at UCSC. Genome Res.12(6):996–1006. http://genome.ucsc.edu/), the complexity of the DMD gene can be seen. It contains at least eight independent tissue-specific promoters and two polyadenylation sites. In addition, the RNA is differentially spliced. The gene thus generates a large set of protein isoforms. The nearby glycerol kinase (GK) gene can occasionally be lost together with DMD in a contiguous gene deletion. Interestingly, although DMD is the largest gene identified to date at the genomic level, its encoded protein, dystrophin (3685 amino acids) is not the largest protein, which is actually another muscle cell protein named titin (composed of 34,350 amino acids). Titin is encoded by a considerably more compact gene (approximately 281 kb in size at the genomic level).
  • Genetic counselling
  • Fig. 15.4 X-linked recessive trait in a family, with obligate carriers (OC) indicated (in a condition which, unlike DMD, does not preclude reproduction).
  • Becker muscular dystrophy
  • Other general points
  • Neurofibromatosis type 1
  • Fig. 15.5 Café au lait patches (coffee-coloured macules) on the skin of Stewart, an 18-year-old catering assistant, who visits a dermatologist. He has eight of these pigmented skin patches (measuring 2–5 cm in diameter) on his abdomen and limbs, as well as three small (1 cm diameter) soft lumps just beneath his skin. He is otherwise apparently healthy. His mother had considerable difficulties with arithmetic, reading and writing at school and has several similar pigmented cutaneous patches, although she was unaware of their possible significance. There is no other family history of note. Stewart’s dermatologist suspects that he may have NF1 and refers him to the genetics clinic for further advice. See question 7 in Self-assessment. Image kindly provided Dr Margo Whiteford, Ferguson-Smith Centre for Clinical Genetics, UK.
  • Fig. 15.6 Neurofibromas on the skin of an individual with NF1. The scar from previous spinal cord decompression surgery is visible at the top of the image.
  • Table 15.2 Diagnostic criteria for NF1 based on the findings of the NIH Consensus Development Conference, 1988 (see review on NF1 in the GeneReviews website for further information)
  • Fig. 15.7 Lisch nodules visible on the iris of a patient affected by NF1. Image from http://www.nature.com/eye/journal/v19/n3/fig_tab/6701478f1.html. Reprinted with permission from Nature Publishing Group: P Cackett, J Vallance and H Bennett; Neurofibromatosis type 1 presenting with Horner’s syndrome, Eye 19:351–3; copyright 2005.
  • The gene and its mutations
  • Genetic counselling
  • Other general points
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • Fig. 15.8 In this family, two individuals have been diagnosed with DMD, Jason (II:5), who died at the age of 25, and Mark (III:3), who is just 15. Mark’s sister, Helen (III:2), hopes to have a child soon and seeks genetic counselling first. See questions 4–6 in Self-assessment.
  • CHAPTER 16 Strong family history–other inheritance mechanisms
  • Key Topics
  • Introduction
  • Myotonic dystrophy
  • Fig. 16.1 Mother and child with myotonic dytrophy.
  • Fig. 16.2 Electropherograms showing the results of TP-PCR from (a) a patient with two small normal-range DMPK alleles and (b) a patient affected by DM. For TP-PCR, one of the PCR primers used consists of DMPK-specific sequence but the other is designed to bind to the CTG triplet repeat itself. In (a), a small range of product lengths is generated, reflecting the slightly differing binding positions of the (CTG)n-binding primer. In (b), however, there is a much greater range of PCR product lengths (along the x-axis) as a result of the presence of a large mutant allele. As a fluorescent dye is attached to one of the TP-PCR primers, the products can be detected by an automated DNA sequencer. The green trace visible in (b) should be ignored for this analysis. Figures adapted from images kindly provided by Dr Alexander Cooke, Institute of Medical Genetics, Glasgow, UK.
  • Fragile X syndrome
  • Fig. 16.3 Typical facies of an individual affected by fragile X syndrome.
  • Fig. 16.4 DNA analysis of a family with fragile X syndrome. Note instability of the larger (mutant) allele. Direction of DNA migration was from top to bottom.
  • Mitochondrial disorder
  • Imprinting-related disorder
  • Fig. 16.5 Model of normal and abnormal gene expression control by the Prader–Willi syndrome (PWS)/Angelman syndrome (AS) imprinting centre (IC). Black circles represent sites of CpG methylation. Arrows indicate transcriptional control. The PWS/AS IC contains two functional regions: the ‘PWS shortest region of overlap’ (PWS-SRO) and the AS-SRO. Normally, on the paternally inherited chromosome 15, the PWS-SRO is unmethylated and active. It activates transcription of the SNRPN, MKRN3, MAGEL2 and NDN genes (shaded blue), while in the brain it suppresses expression of the UBE3A gene (shaded red) possibly via antisense transcription of it. On the normal maternal chromosome 15, PWS-SRO is methylated and inactivated by a mechanism that depends on the presence of AS-SRO on the same chromosome. Consequently, the pattern of gene expression is reversed. In PWS patients with IC PWS-SRO microdeletions, a maternal gene expression pattern results, with loss of SNRPN, MKRN3, MAGEL2 and NDN transcription. In AS patients with IC microdeletions that remove the AS-SRO, on maternal transmission the PWS-SRO fails to undergo methylation and inactivation, leading to the paternal regulatory pattern with loss of UBE3A expression. Modified from Horsthemke and Wagstaff, 2008 (see Further reading).
  • Chromosomal translocation
  • Table 16.1 Risks of chromosomally unbalanced offspring, at birth, for carriers of balanced structural rearrangements. See Gardner and Sutherland (2004) in Further reading for further details
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • Fig. 16.6 A 19-year-old woman (individual III: 4), at 7 weeks’ gestation in her first pregnancy, mentions to her general practitioner in the UK that she had heard that her sister (III: 2) was recently diagnosed in New York State with DM. On questioning, it transpires that their father (II: 1) and his mother (I: 2) were both affected by cataracts in their adult life. On further discussion, the 19-year-old herself mentions a difficulty she has noticed in letting go of shopping bag handles, particularly in cold weather. She asks whether she might be affected by the same condition as her sister and whether there are any tests that could help determine this. She also asks whether, if she is affected, her unborn child may be affected (see Self-assessment question 1).
  • Fig. 16.7 Carol (II: 2), a 26-year-old teacher, seeks genetic advice prior to marrying her partner, to whom she is not related. She is healthy and studied mathematics at university, but is aware that two of her three brothers (II: 3 and II: 4) have required special schooling on account of their significant learning difficulties. She is concerned that there might be a familial tendency that could have implications for her future children. It has transpired that one of Carol’s affected brothers (II: 3) was recently tested and was found to possess a fragile X gene alteration with a product size corresponding to approximately 220 CGG repeats. Carol herself has now undergone genetic testing and has been found to possess 104 repeats. She asks about her risk of having affected children and whether prenatal testing can be relied upon to detect which children are going to be affected (see question 2 in Self-assessment).
  • Fig. 16.8 A 25-year-old man, Arthur (II: 6), is investigated on account of progressive central visual loss. He is aware that his two elder brothers (II: 3 and II: 5) became progressively affected by a similar condition from around the age of 30 and are now legally blind. In addition, his sister (II: 4) has been affected but to a much milder extent. Arthur has a central scotoma and undergoes blood DNA testing for Leber hereditary optic neuropathy. He is found to possess the m.11778G>A mutation in his mitochondrial DNA. Arthur’s parents, now divorced, have each married new partners and had further children (see question 3 in Self-assessment).
  • Fig. 16.9 A male neonate (II: 2) is investigated on account of difficult feeding with a poor suck, severe floppiness, hypogonadism and small hands. His saliva is noted by a junior doctor as being unusually ‘stringy’ and thick. His elder sister (II: 1) has moderate learning difficulty but has never been fully investigated. The baby boy is suspected to have Prader–Willi syndrome and undergoes genetic testing. His karyotype and FISH studies are found to be normal with no detectable deletion at 15q11–13. Methylation analysis does, however, reveal an abnormality with, very unusually, the paternal chromosome carrying a maternal imprint. Following analysis of his DNA, he is subsequently found to possess an imprinting centre microdeletion at the 5′ end of the SNRPN locus on chromosome 15. His mother (I:2), and subsequently his older sister, are both found to possess the same microdeletion. His parents are concerned that their next child might be similarly affected (see question 4 in Self-assessment).
  • Fig. 16.10 Colin and his wife, Ann (II: 2), attend the genetics clinic after being referred by Ann’s family doctor. The doctor was concerned after hearing that Ann’s sister, Paula (II: 4), had recently (following a previous miscarriage) given birth to an infant with multiple congenital anomalies. This, it emerged, had led to Paula having a chromosome test. The karyotype had, in fact, revealed that Paula was a carrier of an apparently balanced translocation between chromosomes 11 and 22, known as t(11;22)(q23;q11). Ann is tested at the genetics clinic and unfortunately is found to possess the same translocation. She is concerned that she may never be able to have a healthy child and seeks advice (see question 5 in Self-assessment).
  • CHAPTER 17 Screening for disease and for carriers
  • Key Topics
  • Introduction
  • Table 17.1 Principles of a screening programme
  • Table 17.2 Screening test sensitivity, specificity and predictive values
  • Prenatal screening
  • Neural tube defect
  • Fig. 17.1 MSAFP in normal pregnancies and pregnancies affected by neural tube defects. (The distribution is log Gaussian and hence medians rather than means are used). Figure kindly provided by Jenny Crossley and David Aitken, Yorkhill Hospitals, Glasgow.
  • Table 17.3 Causes of elevated maternal serum and amniotic fluid AFP
  • Down syndrome
  • Fig. 17.2 Fetal ultrasound scan. The NT measurement between the points indicated by ‘+’ was 2.16 mm.
  • Fig. 17.3 NT measurements in normal pregnancies and in those affected by Down syndrome. Figure kindly provided by Jenny Crossley and David Aitken, Yorkhill Hospitals, Glasgow.
  • Fig. 17.4 Changes in concentrations (shown as multiples of the median or MOM) of four analytes in maternal serum with increasing gestation in pregnancies affected by Down syndrome. Figure kindly provided by Jenny Crossley and David Aitken, Yorkhill Hospitals, Glasgow.
  • Table 17.4 Examples of methods used to screen for Down syndrome
  • Table 17.5 Variations in protein levels in maternal serum in chromosomally abnormal pregnancies
  • Neonatal screening
  • Table 17.6 Examples of conditions that are included in neonatal screening programmes
  • Table 17.7 Signs in infants with congenital hypothyroidism at the time of diagnosis by newborn screening
  • Cystic fibrosis
  • Fig. 17.5 Neonatal screening strategy in Scotland for the detection of CF by immunoreactive trypsinogen (IRT) and mutation analysis. The cut-off values used (indicated by*) are currently 60 ng/ml and 70ng/ml, depending on the stage of the test in the protocol. The strategy has been simplified slightly for illustrative purposes. Figure adapted from details provided by Joan Mackenzie and Arlene Brown, Yorkhill Hospitals, Glasgow.
  • Carrier detection in the adult population
  • Table 17.8 Examples of population groups for which carrier screening is most appropriate
  • β-Thalassaemia
  • Tay–Sachs disease
  • Haemochromatosis
  • Presymptomatic screening of adults
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • Fig. 17.6 A healthy couple are referred to the genetics clinic after their daughter, Fiona (individual III: 1), is found on genetic testing to be homozygous for the δF508 CFTR mutation. She was tested after elevated serum immunoreactive trypsinogen (IRT) levels were detected on routine neonatal screening. See question 2 in Self-assessment.
  • CHAPTER 18 Family history of one or more congenital malformations
  • Key Topics
  • Introduction
  • Table 18.1 Classification and birth frequency of congenital malformations and deformations
  • Fig. 18.1 Frequency of major congenital malformations.
  • Table 18.2 Examples of minor congenital malformations
  • Aetiology
  • Table 18.3 Aetiology of major congenital malformations
  • Fig. 18.2 (a, b) A child with microcephaly. The ears look relatively large as the head is so small.
  • Table 18.4 Causes of congenital deformation
  • Table 18.5 Examples of congenital deformation
  • Chromosomal disorders
  • Fig. 18.3 Frequency of chromosomal abnormalities.
  • Table 18.6 Chromosomal findings in early spontaneous abortions
  • Table 18.7 Chromosomal disorders in newborns
  • Trisomy 21 (Down syndrome)
  • Table 18.8 Frequency of trisomy 21 at birth and at prenatal diagnosis in relation to maternal age
  • Fig. 18.4 Trisomy 21 phenotype. (a) Facies. (b) Single palmar crease in affected fetus.
  • Aetiology
  • Fig. 18.5 Trisomy 21 karyotype. A 34-year-old woman seeks genetic advice following the birth of a girl with Down syndrome. Chromosome analysis performed neonatally has revealed this karyotype. There is no other family history suggestive of chromosome abnormalities. See question 2 in Self-assessment.
  • Recurrence risk
  • Table 18.9 Risks of chromosomally unbalanced offspring (at amniocentesis) for carriers of balanced structural rearrangements. See Table 16.1 for risks at birth.
  • Prenatal diagnosis and screening
  • Trisomy 18 (Edwards syndrome)
  • Fig. 18.6 Trisomy 18 phenotype. (a) General view. (b) Close-up of hand showing characteristic posture.
  • Trisomy 13 (Patau syndrome)
  • Fig. 18.7 Trisomy 13 phenotype.
  • Triploidy
  • Fig. 18.8 Triploidy showing (a) trunk-to-head disproportion and (b) syndactyly. (c) Partial hydatidiform changes in the placenta.
  • Neural tube defects
  • Fig. 18.9 Anterior abdominal wall defects. (a) Exomphalos. (b) Gastroschisis. (c) Body stalk anomaly.
  • Table 18.10 Classification of anterior abdominal wall defects
  • Fig. 18.10 NTDs. (a) Anencephaly. (b) Encephalocele. (c) Open spina bifida. (d) Closed spina bifida.
  • Fig. 18.11 (a, b) Meckel syndrome showing polycystic kidneys, polydactyly and encephalocele.
  • Teratogenic effects
  • Table 18.11 Recognised human teratogens
  • Fig. 18.12 Facies in the fetal alcohol syndrome.
  • Multiple malformation syndromes
  • Fig. 18.13 Potter sequence due to bilateral renal agenesis. (a) Characteristic facies. (b) Amnion nodosum.
  • Fig. 18.14 Prune belly appearance secondary to fetal obstructive uropathy.
  • Fig. 18.15 (a, b) Noonan syndrome. A child possessing a mutation in the SOS1 gene, which, in Noonan syndrome, is less commonly mutated than the PTPN11 gene but which encodes a protein that participates in the same growth factor signalling pathway (see Fig. 18.16).
  • Fig. 18.16 The growth factor signalling pathway involved in the pathogenesis of Noonan syndrome. Redrawn with modifications from Tidyman and Rauen (2008), with permission from Cambridge Journals; see Further reading.
  • Fig. 18.17 (a, b) X-linked hydrocephalus. Note the characteristic adducted hypoplastic thumb in an affected male. (c) Example of a pedigree of a family with X-linked hydrocephalus.
  • Fig. 18.18 Examples of limb defects. (a) Postaxial polydactyly. (b) Syndactyly. (c) Transverse limb amputation due to an amniotic band. (d) Radial aplasia. (e) Ectrodactyly. (f) Phocomelia. (g) Amelia.
  • Fig. 18.19 De Lange syndrome.
  • Fig. 18.20 Hands of a boy who was investigated on account of learning difficulties and a history of a ventricular septal defects and truncus arteriosus. Hypocalcaemia was detected neonatally. The presence of unusually long and tapering fingers was noted by a junior doctor. The karyotype analysis was normal but, on fluorescence in situ hybrisation, a microdeletion at 22q11 was detected. There was no notable family history. The parents sought genetic counselling. See question 6 in Self-assessment. Courtesy of Margo Whiteford, Yorkhill Hospitals, Glasgow.
  • 22q11 microdeletion syndrome
  • Fig. 18.21 Extent of the region of approximately 3 Mb on 22q that is most commonly deleted in patients with velocardiofacial syndrome (VCFS) and DiGeorge syndrome (DGS). The positions of the TBX1 and CRKL genes are marked with orange-coloured boxes. It is believed that loss of one copy of TBX1 is the major contributor to the clinical phenotype, with CRKL acting as a possible modifier. Modified from the UCSC genome browser (http://genome.ucsc.edu). Kent et al. (2002) 12(6):996–1006.
  • Fig. 18.22 Model for the generation of 22q11.2 microdeletion and microduplication by interchromosomal homologous recombination between DNA repeats. Redrawn (not to scale) with permission, from Portnoi, 2009; see Further reading.
  • Other microdeletion disorders
  • Fig. 18.23 Williams syndrome. In this syndrome, there is often short stature, learning disability, transient hypercalcaemia, supravalvular aortic stenosis and a characteristic facial appearance (with prominent lips and an anteverted small nose).
  • Assessment of a child with multiple malformations
  • Table 18.12 Examples of conditions that may be caused by chromosomal microdeletions (e.g. 1–3Mb in size)
  • SUMMARY
  • FURTHER READING
  • WEBSITES
  • Self-assessment
  • Fig. 18.24 Family from the West of Scotland in which the consultand (II: 3), aged 19 (indicated with the arrow), seeks advice as she has recently married and wishes to start a family. Her elder sister (II: 2) was born with spina bifida but no other medical problems. No other individual has been similarly affected in the family. See question 4 in Self-assessment.
  • Fig. 18.25 Family in which a male child (II: 3) is found neonatally to have the genital abnormality known as hypospadias. Subsequently, he is noted to be affected by developmental delay and to have an unusual facial appearance with a short nose, a smooth philtrum and a thin upper lip. The mother has epilepsy and was advised to continue taking her medication of sodium valproate during the pregnancy, as she had done during her previous pregnancies. It transpires that the boy’s elder sister (II: 1) has mild developmental delay and a similar facial appearance, but there is no other family history of such problems. See question 5 in Self-assessment.
  • Part 3 Electronic Databases – A User’s Guide
  • CHAPTER 19 Electronic databases–a user’s guide
  • Key Topics
  • Introduction
  • CASE I
  • Finding information regarding specific conditions and names of associated genes
  • Table 19.1 Clinical information
  • Fig. 19.1 OMIM home page. Searching by name of condition. Online Mendelian Inheritance in Man, OMIM™. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD) {9 June 2010}. Available from: http://www.ncbi.nlm.nih.gov/omim/.
  • Fig. 19.2 OMIM search results, after typing ‘optic atrophy type 1’ into the search box in the OMIM home page shown in Fig. 19.1 and clicking on ‘Go’.
  • Fig. 19.3 OMIM disease-related article, after clicking on ‘#165500’. Clicking on the GeneTests link, if displayed in the top right of the page in OMIM, is a quick route to the relevant GeneReview.
  • Fig. 19.4 GeneReviews search page.
  • Fig. 19.5 GeneReviews article on the condition.
  • Fig. 19.6 GeneReviews list of ‘Resources’, such as patient support groups. This information can be reached by clicking on ‘Consumer Resources’ from the menu on the right side of the GeneReviews article.
  • Laboratories undertaking genetic testing
  • Table 19.2 Directories of gene testing laboratories
  • Fig. 19.7 UKGTN search page (after clicking on ‘Search’ and ‘By Disease or Gene’ at the top of the home page). © UKGTN 2001–2010. All rights reserved.
  • Fig. 19.8 EDDNAL search page (reached by clicking on ‘Search’ on the home page). © EDDNAL 2010.
  • Fig. 19.9 GeneTests Laboratory Directory (reached from the GeneTests home page by clicking on ‘Laboratory Directory’).
  • Patient information and support groups
  • Table 19.3 Patient support directories
  • CASE II
  • Gene-and protein-specific sequence, structure, function and expression information
  • Table 19.4 Scientific information regarding genes and proteins
  • Table 19.5 Tools for DNA or protein sequence analysis
  • Ensembl database
  • Fig. 19.10 Ensembl genome browser. Reproduced with kind permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading. Available from: http://www.ensembl.org/index.html.
  • Finding one’s way through Ensembl
  • Fig. 19.11 Navigation flowchart summarising the paths through various useful pages within the Ensembl database.
  • Coding sequences and transcripts
  • Fig. 19.12 Ensembl Results Summary after selecting ‘Human’ from list and typing ‘ARPKD’ (for autosomal recessive polycystic kidney disease) into the search box at the top of the page. Reproduced with kind permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.13 Ensembl genome browser search ‘Result in Detail’. The details shown may be more abbreviated than those shown here. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.14 Ensembl gene summary for PKHD1. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.15 Transcript summary, obtained after clicking on the transcript ID for the first transcript listed. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Protein domains
  • Fig. 19.16 Protein summary reached after clicking on the protein ID for the first transcript listed. Reproduced with kind permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.17 Sequence of exons for a particular transcript, obtained by selecting ‘Exons’ from the list on the left after selecting a specific transcript ID to view. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.18 Amino acid sequence of a protein encoded by a specific transcript. Reached by clicking on ‘Protein’ on the left, while in the Transcript Summary page. To display the features shown, it is then necessary to select ‘Configure this page’, switch on the display of numbering and variants and, finally, click on the ‘save and close’ tick in the top right. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.19 Marked up genomic sequence, showing exons (in colour) and introns. Reached from the Gene summary page by clicking on ‘Sequence’ at its extreme left. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.20 List of homologues of the same gene in other species (obtained by clicking on ‘Orthologues’ from the Gene Summary page. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.21 Alignment between human and armadillo PKHD1 gene sequences, (reached by clicking on ‘Alignment’ within the Ensembl Identifier column of the table of orthologues. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • BLAT/BLAST searches
  • Fig. 19.22 BLAT/BLAST search in Ensembl. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.23 Results of BLAT/BLAST search in Ensembl. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.24 Ensembl ‘Region in detail’ page (reached by clicking on the ‘location’ tab near the top of the ‘Gene summary’ page, or by clicking on the “C” link at the bottom left corner of the BLAT/BLAST results page. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • GeneCards website
  • Fig. 19.25 GeneCards homepage. With permission from the Weizmann Institute of Science.
  • Fig. 19.26 GeneCards search results. With permission from the Weizmann Institute of Science.
  • Fig. 19.27 First part of GeneCard for PKHD1, showing alternative names and the gene’s chromosomal and genomic location. With permission from the Weizmann Institute of Science.
  • Fig. 19.28 Expression data for PKHD1 in GeneCards, obtained from microarray analysis (GeneNote and GNF) and electronic prediction (eNorthern). The relatively high level of expression in the kidney is visible. With permission from the Weizmann Institute of Science.
  • Gene expression data
  • CASE III
  • Nucleotide sequences and human mutations
  • Table 19.6 Mutations and SNPs
  • Automatic primer design tools
  • Table 19.7 Websites useful when designing primers
  • Fig. 19.29 Primer3Plus. © 2006, 2007 by Andreas Untergasser and Harm Nijveen.
  • Fig. 19.30 Genomic Primers (for selection of multiple primer pairs). © 2003 Erasmus MC Rotterdam.
  • Checking for SNPs
  • Fig. 19.31 Configuration page in Ensembl for ‘Marked up gene sequence’, in order to show SNPs. This page is reached by clicking on ‘Configure this page’, after clicking on ‘Sequence’ from the ‘Gene summary’ page. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.32 Marked-up gene sequence, now configured to display variants (with links) and line numbering. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.33 ‘Variation summary’ page reached by clicking on the hyperlink to the right of a SNP in ‘Marked up gene sequence’ view. Reproduced with permission of the Wellcome Trust Sanger Institute. See Flicek et al. (2010) in Further reading.
  • Fig. 19.34 Further information from dbSNP reached by clicking on the dbSNP link near the top of the ‘Variation summary’ page.
  • Checking of primers for specificity
  • Fig. 19.35 Reverse e-PCR search facility at NCBI (after selecting Table Input). It performs a virtual PCR, checking the specificity of the primer pair.
  • CASE IV
  • Displaying map data for genes and markers
  • The UCSC genome browser
  • Fig. 19.36 UCSC Genome Browser ‘Gateway’. This and following figures from http://genome.ucsc.edu/ (Kent WJ, et al., 2002. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996–1006).
  • Fig. 19.37 Selection of gene from the list of search results in UCSC. Source: http://genome.ucsc.edu (Kent et al., 2002 in Further Reading).
  • Fig. 19.38 UCSC Genome Browser window opened by clicking on ‘Other genome browser: UCSC’ (from menu at left of Ensembl’s ‘Region in detail’ screen). It can also be reached by searching using the UCSC Genome Browser ‘Gateway’ and zooming out as shown. Source: http://genome.ucsc.edu (Kent et al., 2002 in Further Reading).
  • Displaying microsatellite markers
  • Fig. 19.39 UCSC Genome Browser window after clicking on ‘zoom out × 10’ to widen the genomic region viewed on screen. Source: http://genome.ucsc.edu (Kent et al., 2002 in Further Reading).
  • Fig. 19.40 UCSC Genome Browser window after choosing ‘include’ Genethon markers from the drop-down list and then clicking on ‘submit’. Source: http://genome.ucsc.edu (Kent et al., 2002 in Further Reading).
  • Fig. 19.41 STS marker details in UCSC database, obtained after clicking on the small black vertical line (in the upper part of the window) representing, for example, STS Marker AFMB044XE9. Source: http://genome.ucsc.edu (Kent et al., 2002 in Further Reading).
  • CASE V
  • Online missense mutation analysis tools
  • Table 19.8 Websites providing analysis of possible functional significance of missense (amino acid substitution) mutations
  • Fig. 19.42 List of matching results after typing ‘neurofibromin’ into the search box at the top right of the PDB home page. Source: RCSB PDB (www.pdb.org); Scheffzek et al., 1998 in Further Reading.
  • Fig. 19.43 The GAP-related domain of neurofibromin, viewed in 3D (and can be enlarged, rotated and annotated by right-clicking and selecting various options). Source: RCSB PDB (www.pdb.org). Scheffzek et al., 1998 in Further Reading.
  • Fig. 19.44 Coloured view obtained by selecting via right-clicking: colour/structures/cartoon/by-scheme/amino-acids. Source: RCSB PDB (www.pdb.org). Scheffzek et al., 1998 in Further Reading.
  • CASE VI
  • Computer-aided syndrome diagnosis
  • Table 19.9 Websites for computer-aided syndrome diagnosis
  • Fig. 19.45 Winter–Baraitser Dysmorphogy Database (London Medical Databases) software package. With permission from London Medical Databases.
  • Fig. 19.46 Finding clinical features within the ‘Search Syndromes on Features’ search window. With permission from London Medical Databases.
  • Fig. 19.47 Search window ‘Search Syndromes on Features’ within the Winter–Baraitser Dysmorphogy Database software package. With permission from London Medical Databases.
  • Fig. 19.48 Search results within the Winter–Baraitser Dysmorphogy Database software package. With permission from London Medical Databases.
  • Fig. 19.49 OMIM home page.
  • Fig. 19.50 Search results using OMIM.
  • Fig. 19.51 OMIM description of the syndrome.
  • Fig. 19.52 GeneTests page reached after clicking on the blue ‘Genetests’ link at the top right of the page.
  • Fig. 19.53 GeneReview for genetic condition.
  • Fig. 19.54 Phenomizer online search. Selecting clinical features to add to the ‘Patient’s Features’ list. Reproduced with kind permission of Sebastian Köhler from the Phenomizer website. See Köhler et al., 2009, in Further reading.
  • Fig. 19.55 Phenomizer online search page after adding specific clinical features to the Patient’s Features list. Reproduced with kind permission of Sebastian Köhler from the Phenomizer website. See Köhler et al., 2009, in Further reading.
  • Fig. 19.56 Phenomizer online search. Results list obtained after clicking on ‘Get diagnosis’. Reproduced with kind permission of Sebastian Köhler from the Phenomizer website. See Köhler et al., 2009, in Further reading.
  • CASE VII
  • Professional genetics societies
  • Table 19.10 Genetics societies
  • The Human Genome Project: ethics and education
  • Table 19.11 Human Genome Project: ethics and education
  • FURTHER READING
  • Self-a ssessment
  • Back Matter
  • Self-assessment – answers
  • Chapter 1
  • Chapter 2
  • Chapter 3
  • Chapter 4
  • Chapter 5
  • Chapter 6
  • Chapter 7
  • Chapter 8
  • Chapter 9
  • Chapter 10
  • Chapter 11
  • Chapter 12
  • Chapter 13
  • Chapter 14
  • Chapter 15
  • Chapter 16
  • Chapter 17
  • Chapter 18
  • Chapter 19
  • APPENDIX 1 Odds, probabilities and applications of Bayes’ theorem
  • Fig. A1.1 Pedigree of a family with Duchenne muscular dystrophy.
  • Table A1.1 Bayes’ calculation – 1
  • Table A1.2 Bayes’ calculation – 2
  • APPENDIX 2 Calculation of the coefficients of relationship and inbreeding
  • Fig. A2.1 Pedigree example of calculation of coefficient of relationship.
  • Fig. A2.2 Consanguineous pedigree with a single-gene disorder.
  • APPENDIX 3 Population genetics of single-gene disorders
  • Maintenance of gene frequencies
  • Table A3.1 Allele and genotype frequencies at a locus with two alleles, A and a
  • Table A3.2 Frequencies of different parental genotypes at reproduction
  • Table A3.3 Frequencies of different types of offspring after reproduction
  • APPENDIX 4 Legal aspects
  • Genetic counselling
  • Prenatal diagnosis
  • Consanguinity
  • Paternity testing
  • FURTHER READING
  • Glossary
  • Index