Disease pedigrees and detecting disease alleles

Question 1

Define a malformation?

Answer 1

A morphological abnormality arising from an abnormal developmental process

Question 2

Define Dismorphology?

Answer 2

Recognition and study of birth defects/malformations and related syndromes

Question 3

Define congenital

Answer 3

Present at birth.

Question 4

Define (genetic) syndrome

Answer 4

a recognisable set of developmental abnormalities that probably have a single cause

Question 5

How are consanguinity, miscarriage, stillbirth, termination represented on genetic/disease pedigrees?

Answer 5

Consanginuity is denoted by a double line between the parents.

Miscarriage by a triangle (filled/affected or not)

Termination by crossed triangle.

Stillbirth by crossed gender symbol and SB +gestational age

Question 6

How are Monozygous, or dizygous or uncertain twins indicated?

How is adoption and ongoing pregnancy denoted?

Answer 6

Twins are denoted by a single branching line coming from parents. MZ further connected by a horizontal line. unknown indicated by ‘?’

Adopted children unconnected, broken line. put in ‘brackets’

Ongoing pregnancy is a diamond with a P in it.

Question 7

Important considerations in Autosomal Recessive inheritance?

Answer 7

1) Carrier status of parents.
2) consanguinity: as this can increase the frequency of rare autosomal recessive disorders. If the founder/original recessive disease mutation occurs in an inbred population, it is perpetuated and propagated.

Question 8

Define consanguinity:

And 2nd cousins, 1st cousins once removed

Answer 8

Sexual relations between related partners who are second cousins or closer.

Second cousins have a paternal grandparent related to a maternal grandparent.

First cousins ‘once removed’ indicates a generation gap.

Question 9

Important considerations for autosomal dominant inheritance?

Answer 9

Penetrance: Incomplete penetrance is when not all carriers of dominant mutation express disease phenotype.e.g.HNPCC Age-dependent penetrance is where individuals display phenotype only later in life. e.g.huntingdons.

Expressivity: variation between individuals in severity of a phenotype caused by a mutation.

Anticipation: Worsening of severity of disease over successive generations. (triplet repeat expansion in HD)

Mosaicism: Somatic mosaicism: partial phenotype, where a new mutation in early embryogenesis only ends up some of the cells/tissues of the body. (e.g. in Hemimegalencephaly)

Germline mosaicism: some of the sperm or eggs carry a novel mutation, the parent is unnaffected, but their offspring can be.

Question 10

Why are Y-linked conditions so uncommon?

Answer 10

Because Y-chromosome encodes few genes, and they often relate to male fertility. So whilst a Y-linked disease is passed down **from an affected father to all of his sons **it may affect his or their ability to have children at all.

e.g. non-obstructive spermatogenic failure

Question 11

3 examples of X-linked recessive disorders:

Answer 11

Colour-blindness.

Haemophilia.

X-linked intellectual disability. (e.g. CUL4B-mutated syndromal ID. very common.)

Question 12

X-linked dominant disorders:

1 example?

Answer 12

Typically males (hemizygous) more severely affected, often fatal.

But heterozygous females more commonly seen.

Rett syndrome: common cause of complex regressive neurological disability in girls.

Question 13

What is genomic imprinting?

And how can it lead to disease?

Answer 13

Imprinting is the selective silencing of a maternal or paternal copy/allele of a gene. (by histone modification or DNA methylation) Around 50 known imprinted human genes.

Leading to the other copy being selectively expressed.

This can lead to disease when the selectively expressed allele is mutated/deleted/silenced. Or when the offspring receive 2 alleles from e.g. in Angelman syndrome (similar to Rett syndrome) and Beckwith-wiedemann syndrome. (overgrowth disorder, cancer prone)

Question 14

Example of a gain of function mutation causing disease?

Answer 14

Achondroplasia, mutation constituently active fibroblast growth factor receptor 3 FGFR3. This inhibits chondrogenesis.

Question 15

Example of a dominant negative mutation?

Answer 15

Osteogenesis imperfecta, where mutant collagen impairs function of collagen triple helices leading to brittle bones.

Question 16

3 different types/outcomes of SNP substitution mutation?

Answer 16

Synonymous mutation: amino acid is unchanged

Missense: codes different amino acid

Nonsense: codes stop codon, truncates protein (typically pathogenic)

Question 17

Splice-site mutation?

Answer 17

Mutation in sequence coding for control of splicing introns out of pre-mRNA. Result: exons could be spliced out, introns left in mature mRNA etc.

Question 18

Copy number variation? example

Answer 18

Copy number variation is common, created by gene duplication or deletion. Implicated in many diseases.

Reduced copy number (a deletion) at 22q11 gives DiGeorge syndrome/velocardiofacial syndrome. (from haploinsufficiency of a variety of genes)

Mostly spontaneous occurrence

Question 19

Hereditary haemochromatosis?

Answer 19

HH. Autosomal recessive mendelian inheritance pattern. Very common mutant alleles in N european pop.

Excess iron absorption, accumulates in tissues/organs and causes multisystem problems.

Incomplete penetrance (including lifestyle factor influences, and more common in men, who don’t menstruate)

Treatment is simply venesection!

Question 20

How is hereditary haemochromocytosis diagnosed?

Answer 20

Phenotype: high iron levels (ferritin)

maybe organ symptoms like diabetes.

Genotype: PCR amplification of a gene then dideoxynucleotide fluorophore conjugated DNA sequencing of the gene.

Question 21

Restriction fragment length polymorphism?

Answer 21

A cheap and quick technique to identify presence of a known mutation (that happens to create or destroy a restriction endonuclease binding site) if mutation is there, fragments will be different sizes to wild-type.

Question 22

How is Velocardiofacial/DiGeorge syndrome diagnosed?

Answer 22

Phenotype: Cardiac abnormalities, facial malformation, immune and metabolic problems

Genotype: FISH probes, fluorescent in situ hybridisation. Probe for 22q11 commonly deleted sequence (and use a telomere binding control)

Question 23

What else can FISH diagnose (other than CNV in DiGeorge?)

Answer 23

Can identify Bcr-Abl fusion gene in CML (by combination of probe for Bcr and Abl)

Can identify chromosomal translocation (between chromosomes)

Can identify **telomere problems **(such as in spontaneous miscarriages)

Question 24

How to identify novel genomic disorders/CNV?

Answer 24

ACGH: Array Comparitive Genomic Hybridisation

By comparing the whole of a patient’s DNA/chromosome against a control for copy number variation. Essentially probing every single possible area for CNV, more copies = more signal at each fixed probe (relative to control/mean signal)

Question 25

How to identify unknown or novel SNP mutations causing disease?

(such as in the addenbrookes case where they identified an atypical Werners syndrome patient (premature aging/progeria))

Answer 25

Sequence the patients whole genome by using Next-Generation technology to identify all SNPs.

Exclude all SNPs known in databases.

Narrow down to rare homozygous missense/nonsense mutations