session 5 population genetics Flashcards
what criteria determine if a disorder is suitable for screening?
- prevalence known
- treatment available
- effective, safe and simple and ethical test
- clinically well-defined disorder
- significant morbidity/mortality
- intervention improves outcome
- cost-effective
what are potential issues of using genomics in NBS?
- no phenotype
- VUS
- incidental findings
- expensive
- variable age of onset and penetrance
- cost of genetic counselling and follow-up
what is the WHO definition of infertility?
• Failure to achieve a clinical pregnancy after 12 months or more of regular unprotected sexual intercourse (WHO).
• No cause is identified in 25-30% couples = unexplained infertility.
• >80% couples will conceive within 1y
what are non-genetic causes of infertility?
why could it be useful to know the cause?
chemotherapy, smoking, obesity, maternal age, infections, POF + polycystic ovaries, endometriosis, uterine abnormalities, injury, low sperm count
determining cause useful for recurrence risks, prognosis, treatments eg. testicular sperm retrieval
what is the incidence of Recurrent miscarriage, defined as the loss of three or more consecutive pregnancies?
, affects 1% of couples
what proportion of male infertility do genetic factors account for? what are the 4 categories of male infertility?
15%
1. sperm quality
2. sprm quantity
3. obstruction of the ducts
4. Hypothalamic-pituitary disturbance
name sex chromosome abnormalities associated with male infertility (6 options)? what are clinical features?
- Kleinfelter 47, XXY - most frequent cause. 15% are mosaic 47,XXY/46,XY (more likely to have residual sperm). clinical features = hypogonadism, gynecomastia, low testosterone and azoospermia or oligospermia. if there is residual sperm can use ICSI after PGD to achieve pregnancy. hormone replacement therapy can be given. caused by non-disjunction meiosis 1 (male) or meiosis II (female)
- 45,X/46,XY mosaicism - azoospermia and low testosterone levels. 10% have abnormal, ambiguous or female genitalia.
- 46,XX male Disorder of Sex Development (DSD). may have Yp material present (SRY) or XX/XXY mosaicism. 75% have SRY gene present (SRY+) caused by meiosis 1 abnormal exchange. may present with gynecomastia, azoospermia and small testes. 15% have genital ambiguity.
- Y isochromosome 46,X,i(Y) - may be mosaic with 45,X cell line. may be infertile male or female with turner syndrome features and ambiguous genitalia. male infertility due to loss of AZF (Yq11.2)
- x;autosome translocations- spermatogenic arrest due to disruption of the sex vesicle
6.Y;autosome translocations - infertility due to disruption of sex vesicle or disruption of AZF loci. ring & marker chromosomes also disrupt the sex vesicle
how do deletions of the azoospermia factor AZF region occur? (yq11.2)
non-allelic homologous recombination
what genes do AZFa remove? what is the phenotype?
complete deletion (rare) removes USP9Y and DDX3Y. most severe phenotype : Sertoli cell-only syndrome (SCOS), bilaterally small testes and azoospermia. sperm retrieval not possible
what are features of AZFb deletion? what % of AZF deletions does this account for?
5% of deletions. large 6.2Mb deletion removes 32 genes.
azoospermia and sperm retrieval not possible.
what are features of AZFc deletion? what % of AZF deletions does this account for? what genes are removed?
3.5Mb including 12 genes
80% of deletions - less severe
50% have residual sperm for ICSI
Interstitial or terminal deletions that include AZFc only are mediated by recombination between the b2/b4 amplicon repeats and result in a variable infertility phenotype - sertoli cell only syndrome (SCOS). azoospermia or oligozoospermia (reduced sperm count)
- DAZ genes removed (involved in germ cell development). But two other copies on autosomal genes which is why there may be residual sperm. Deletions also reported in fertile males.
how does cftr relate to infertility in males?
what % of these cases have cftr mutations?
how can it be treated?
what is the most likely genotypes of CFTR-relaed disorder causing infertility?
when does p.(Arg117His) cause cf and when does it cause cbavd?
CBAVD or CUAVD results in interference in sperm transport. CUAVD may be fertile or infertile.
caused by CFTR variants in 80% of cases
Almost all males with CF have obstructive azoospermia due to CBAVD
treatment with ICSI
partner should undergo carrier screening
• Isolated CBAVD is a CFTR-related disorder
- majority have one severe and one mild mutation eg. severe+5T ( polyT tract in intron 8 influences efficiency of exon 9 splicing) and remaining have two mild mutations
- • 5T allele not fully penetrant for CBAVD and TG tract length may modify the effect of 5T
• p.(Arg117His) also common – associated with CF when in cis with 5T but CBAVD with 7T/9T
what is primary and secondary amenorrhea
absence of periods. Primary if never had a period or secondary if follows after previously having periods
what is primary ovarian insufficiency (POI)?
the ovaries stop functioning normally before the age of 40y
what proportion of female infertility is caused by genetics?
name syndromes and genetic causes of infertility in females?
10% - chromosomal abnormalities Comprise the largest proportion of cases
Turner syndrome - complete or partially missing X chromosome, . >99% of 45,X conceptuses result in spontaneous loss. short stature, amenhorrea, infertility, congenital heart defects, increased NT. frequently mosaic. Paternal nondisjunction accounts for 70% cases. variable phenotype due to level and distribution of abnormal cell line. structural abnormalities include i(X)(q10), 46,X,+mar , 45,X/46,XX or 45,X/47, XXX , 46, X,del(Xp). give hormone therapy and eostrogen
x;autosome translocation carriers - preferential silencing of normal X so functionally balanced gamete. This skewed X inactivation can reveal recessive X linked diseases eg. DMD. POF associated with breakpoints in CR1 or CR2. If fertile there is risk of unbalanced offspring.
X-X translocations - infertility inevitable
Swyer syndrome - XY females complete gonadal dysgenesis and infertility. • 15% caused by pathogenic variants in SRY
FMR1 - CGG premutation 59-200 repeats POI
46,XX gonadal dysgenesis - primary amenhorrea, POF, hypergonadotrophic hypogonadism, lack of puberty. most cases unexplained
what is the genetic testing strategy for infertility?
- specific phenotype = targeted testing eg. CFTR for CBAVD
- less specific phenotypes = karyotype + Y chr microdeletions in azoospermic male of FMR1 in females with POF
-array for POC after 3rd miscarriage. karyotype parents if unbalanced arrangement in fetus - DSD NGS panel or microarray
what is Congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency?
• CYP21A2 (AR) condition
where lack of 21-hydroxylase activity - excess of androgens produced. infertility
• Amount of functional enzyme determines the severity – salt-wasting type (75%, most severe), simple virilizing type to non-classical CAH
: females gave ambiguous genitalia in salt-wasting and simple virilizing type
- can be detected using non invasive prenatal sexing to determine if fetus is female - administer dexamethosone to reduce masculinisation
what is androgen insensitivity syndrome?
• Loss of function variants in the androgen receptor gene AR Xq12, - XLR
o Complete androgen insensitivity syndrome (CAIS): - : external sex characteristics of females, primary amenorrhea and infertile
o Partial and mild forms have residual sensitivity so can have spectrum of phenotypes from normal female, both male and female or normal male sex characteristics but are often infertile
- also causes SBMA - CAG repeats
what is a Disorder of Sex Development? what are the 3 subtypes?
congenital condition where development of chromosomal, gonadal/ anatomical sex is atypical
1)sex chromosome DSD
2) 46,XY DSD
3) 46, XX DSD
name the 4 sex chromosome DSD
- 45, X turner syndrome and variants
- 47, XXY kleinfelter - (also XXYY and XXXY and XXXXY cause kleinfelter)
- 45, X/46, XY mixed gonadal dysgenesis
- 46 XX/46XY chimeric ovotesticular DSD
name some 46,XY DSD? what are clinical features?
- disorders of testicular development - eg. complete or partial gonadal dysgenesis eg. 46,XY phenotypic female= Swyer syndrome (complete gonadal dysgenesis) - caused by SRY mutation.
Swyer syndrome= ‘streak’ gonads, female external genitalia, failure of pubertal development, infertile
2.disorders of androgen synthesis and action eg. Leydig cell hypoplasia & androgen insensitivity syndrome- caused by AR gene mutations. female external genitalia and infertile.
name some 46,XX DSD?
If phenotypic male - 90% carry SRY gene. usually from X-Y translocation. Hypogonadism + gynaecomastia common. External genitalia range from normal male to ambiguous
- disorders of ovarian development eg. testicular DSD = phenotypic male or gonadal dysgenesis (FSHR mutation) = phenotypic female
- androgen excess eg. Congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency - AR CYP21A2 gene.
46,XX= masculinisation of external genitalia
46,XY= normal male genitalia
• Mother treated with dexamethosone during pregnancy.
• AR disorder of enzymes - increased androgen synthesis.
• Increased androgen synthesis during embryonic development results in virilisation of external genitalia in 46,XX foetuses
what testing is carried out for DSD? which condition is considered a medical emergency?
- QF-PCR + chromosome analysis via karyotype requested to identify chromosome complement
- Panel testing may be appropriate in patients with abnormal sex chr karyotypes if karyotype result does not explain DSD phenotype
considered medical emergency in neonates born with ambiguous genitalia due to potential association with glucocorticoid + mineralocorticoid deficiencies in CAH, + parental anxiety to assign correct sex
• Longer-term patient care= clinical + diagnostic evaluation (assist with gender assignment), surgical management, hormone replacement therapy + psychosocial care
mention 4 genes involved in DSD?
SRY - 46,XX male Disorder of Sex Development (DSD).
SOX9 - gonadal dysgenesis
AR - androgen insensitivity
CYP21A2 - CAH
SF1- gonadal dysgenesis
WT1- gonadal dysgenesis
FOXL2
what is i(Xq)? what disorder can it cause? what gene is missing and what feature does this cause?
why is there no isochromosome of the Xp arm?
Isochromosome for the long arm of the X chromosome
Turner syndrome - loss of PAR1 region on Xp (SHOX)
a mosaic with a normal 46,XX cell line, 45,X cell line, or both - may be fertile
Decreased expression of the SHOX gene in PAR is associated with short stature
No isochromosome of the short arm is viable as XIST would be absent.
what is a ring X chromosome? r(X) what features may be present?
what test should be performed to determine risk of gonadoblastoma?
aberrant chromosome whose ends have fused together to form a ring. usually X material is deleted or duplicated.
Rings can be inherited from mother to daughter but are often present in a mosaic state.
turner syndrome or may be normal - depends on XIST presence and amount of inactivation.
If XIST absent - more severe phenotypes as normal X inactivated and nullisomic for some regions.
FISH should be performed to exclude the possibility that the ring is derived from the Y chromosome - high risk of gonadoblastoma if the ring (or marker) is Y-derived
where is the SHOX gene located? what is it associated with?
xp22 Yp22 PAR1 region
TS
what is MECP2 duplication syndrome ?
what does a mecp2 mutation cause?
moderate to severe intellectual disability
up to 4Mb dup in males
in females, X inactivation means usually normal
MECP2 mutation = rett syndrom (embryonic lethal in males)
what are the pseudo-autosomal regions (PAR1 and PAR2)?
short regions of homology at the tips of the X and Y chromosomes. They allow the X and Y chromosomes to pair and properly segregate during meiosis
Pseudo-autosomal regions escape X-inactivation and so normally expressed from both X chromosomes in females. Two copies of the genes in this region are required in both males and females. The SHOX gene, an important transcription factor involved in formation of many body structures during early embryonic development, is located in the pseudo-autosomal regions
describe how X chromosome inactivation occurs?
how is this affected in x;autosome translocations in females? what disorders might result?
what do x;autosome translocations cause in males?
mediated by the XIST gene in the X inactivation centre (XIC) on Xq13
Inactivation spreads in cis outwards from the XIC. XIST is required to start the process of X inactivation but it is not required for the maintenance of X inactivation
Females with balanced X-autosomal translocations generally show inactivation of the normal X and functional balance is achieved by using both parts of the X in the translocated chromosomes as the active X. However, skewed X inactivation due to a balanced translocation can cause a phenotype, for instances, in Duchenne muscular dystrophy. A phenotype can occur due to reduction from biallelic to monoallelic expression
Translocations with breakpoints in Xq13-q22 and Xq22
Balanced X-autosomal translocations in males invariably lead to male infertility, due to spermatogenic arrest.
Male infertility: AZF deletion found and there were 2 X. and write the possible karyotype AND possible explanation
47,XX,del(Y)(q11)? 47,XX,+idic(Y)(q11.21)?
describe variant Y chromosomes? (no clinical consequence)
- Variation in the length of the Yqh region (Yq12) - heterochromatin. normal phenotype
- Pericentric inversion Y
- Satellited Yq (Yqs): Due to translocation of the p arm of acrocentric chromosomes (usually chr 15) to Yqter
- Y heterochromatin translocations: C band material from Yq tranlocated onto the short arm of an acrocentric
what Y chromosome rearrangements are pathogenic?
Yp-, Yq-, iYp, idicYp, iYq, idicYq
If there is 45,X mosaicism, genital development may be male, female or ambiguous
Absence of SRY (Yp11.2) leads to female development and loss of other Yp loci (eg.PAR1-SHOX) determines a Turner syndrome phenotype
Y;Autosome translocations - what feature results? what do the majority of these translocations involve?
- lead to male infertility as cause spermatogenic arrest
- autosomal components of the quadrivalent are dragged into the sex vesicle and can have a sabotaging effect disrupting meiosis
- Infertility also seen if the breakpoint is at Yq11 and disrupts AZF regions
- 70% of Y;Autosome translocations have Acrocentric p arm and Yq heterochromatin
- some involve Yp SRY translocation to an autosome
X-Y translocations - what is the most common and how does it arise? which gene is deleted from xp22? what is the phenotype in males?
most frequent = t(X;Y)(p22.3;q11)
NAHR at spermatogenesis of the female carrier’s father
deletion of Xp22 = loss of SHOX
Infertility in males
what does Xp;Yp translocation result in? (which gene is transferred) how does it arise? what is the consequence?
46, XX males
transfer of SRY onto an almost intact X chromosome
abnormal XY recombination during paternal meiosis
males are invariably infertile
o If SRY gene missing may have female phenotype.
what is a ring Y chromosome? r(Y) what features may be present?
aberrant chromosome whose ends have fused together to form a ring
Male (SRY intact) with sexual infantilism (lack of sexual development), ambiguous genitalia, short stature
• Symptoms seen in patients carrying ring chromosomes are more likely to be caused by the deletion of genes in the telomeric regions of affected chromosomes
• Associated with 45,X cell line in 70% cases
Isochromosome Y - what two options are there and what are clinical features?
i(Yp) - males: microcephaly, hypogonadism, short stature
i(Yq) - lack SRY - normal female but with sexual infantilism, TS features, short stature
what is the most frequent structural abnormality of Y chromosome? what two types are there and what are features?
Isodicentric Y
• Instability during cell division - leads to 45, X
females = TS features males = infertility
• Idic(Yp) -
1/3 phenotypically male with clinical features that include small, abnormal or asymmetrical testes, azoospermia, incomplete masculinisation of external genitalia, short stature, TS like features, ambiguous genitalia
2/3 phenotypically female with streak gonads, enlarged clitoris, short stature, TS like features
• Idic(Yq) -
1/3 phenotypically male with clinical features that include small testes, asymmetrical gonads, azoospermia, hypospadias, short stature, TS like features
o ~1/3 intersex with ambiguous external genitalia, hypospadias, abnormal gonads, inguinal/immature testes, short stature, gonadoblastoma
o ~1/3 phenotypically female with streak or asymmetrical gonads, abdominal testes, TS like features, short stature
what is triploidy? what is the prognosis?
what is recurrence risk?
additional set of chromosomes resulting in a count of 69 (3n)
3% of pregnancies but >99.9% spontaneously abort
poor prognosis (survival <1 month)
~1% recurrence
what is Diandry (also referred to as type I triploidy)?
partial hydatidiform mole
how might they form?
what are features?
• Double paternal contribution i.e. two paternal sets and one maternal set of chromosomes eg. 69, XXY, 69,XXX or 69,XYY
- most common form of triploidy
- • Majority as a result of fertilisation of a normal egg by 2 sperm (dispermy)
• Minority as a result of fertilisation of a normal egg by a diploid sperm (complete non-disjunction) or duplication of chromosomes in a single sperm after fertilization of a normal egg
IUGR, neural tube defects, Oligohydramnios (too little fluid), Large placenta (cystic), later on - syndactyly (webbed fingers or toes) and hydrocephaly (fluid on brain)
*69,YYY not viable
what is Digyny (also referred to as type II triploidy)?
Placenta is non molar and generally small
how might they form?
what are fearures?
• Double maternal contribution i.e. two maternal sets and one paternal set of chromosome
• Fertilisation of a diploid egg (nondisjunction of entire chromosome set at MI or MII) by a haploid sperm
• Retention of a polar body in a fertilised egg
• Fertilisation of an ovulated primary oocyte (46 chromosomes)
• Fusion of 2 eggs (dieggy) and fertilisation by a haploid sperm
IUGR, small placenta, large head, Oligohydramnios (too little fluid), Holoprosencephaly (failure of forebrain to divide).
what is a Hydatidiform Mole
• Most common form of gestational trophoblastic disease (GTD) - produce human chorionic gonadotrophin (hCG) which can be measured
- pre-malignant forms are complete or partial hydatidiform moles
- most can be successfully treated and cured if diagnosed early
what is a complete mole? how can it be formed? what does it cause? what are clinical features?
- Only paternal chromosomes; diploid
- 90% =empty egg fertilised by single sperm and then duplicated to give 46, XX
- 10% = empty egg + two sperm to give 46, XX or 46, XY
- loss of mat chromosomes from first cleavage
- excess paternal material and lack of maternally imprinted genes leads to trophoblastic hyperplasia
- No formation of a fetus or embryo
symptoms = hypertension, oedema (fluid) and vaginal bleeding, increased uterus size, risk of trophoblastic disease
*46,YY not viable
how are molar pregnancies diagnosed? what are the symptoms? how is it treated?
• Blood tests will show very high levels of hCG
- ultrasound scan - the mole resembles a bunch of grapes
- • A definitive diagnosis requires histopathological examination
painless vaginal bleeding in the fourth to fifth WEEK of pregnancy and more vomiting than expected, Pelvic pressure or pain, high blood pressure
treatments: Suction evacuation , monitor hCG levels, • Chemotherapy recommended if Metastases identified or rising levels of hCG
what is the recurrence risk of molar pregnancy
1% or up to 5% risk following two consecutive complete moles
• Recurrence can be either of the same (complete or partial) or of the other type
how is Familial recurrent hydatidiform moles (FRHM) inherited?
when would you test for this disorder?
AR very rare predisposition to recurrent molar pregnancies
• Women with this condition are very unlikely to achieve any normal healthy pregnancies
• Homozygous and compound heterozygous mutations in two genes are known to be associated with FRHM; NLRP7 at 19q13.42 (OMIM: 609661) and KHDC3L at 6q13 (OMIM: 611687)
- test for this disorder if recurrent complete hydatidiform moles
Xp deletion in a male - mention gene, other tests you could do, clinical symptoms?
SHOX - Xp22.33
short stature
Leri-Weill dyschondrosteosis (LWD) - short stature, scoliosis,
FISH, array, karyotype
translocation involving X autosome - pachytene and label different parts and mention outcomes and what would be the most viable
https://doctorlib.info/medical/chromosome/5.html
X, 12, der(X) - with centromere, der(12) - with centromere
2:2 = normal or balanced
adjascent 1 (1 of each centromere) - functional X disomy OR functional autosome disomy
adjascent 2 (2 of each centromere)
eg. 46,X,der(X) karyotype from adja-cent-1 segregation
eg. 46,-X,X,+der(10) karyotype - adjascent 2
3:1
tertiary trisomy = 2 normals, one rearranged
interchange trisomy = 2 rearranged, one normal
4:0 unviable.
what is point of care testing and what are benefits?
o Near or at the patient site e.g., blood glucose
can be performed by clinical staff without laboratory training or by the patient themselves
o Rapid, cheaper results to inform medical management
eg. ParaDNA testing - BRCA1/2 founder mutations in 1hr. goof for poor regions
what is direct to consumer testing?
ordered by the person - genetic info to make predictions on health, kinship and ancestry. usually SNP array or NGS
what is population screening?
Screening refers to the use of simple tests across an apparently healthy population in order to identify individuals who have risk factors or early stages of disease, but do not yet have symptoms
how does genetic screening differ from genetic testing?
Genetic screening differs from genetic testing in that it targets populations/sub-populations rather than at-risk individuals to detect future disease risks in individuals/progeny for which established preventive interventions exist (e.g. newborn screening for phenylketonuria and cystic fibrosis, carrier screening for sickle cell disease).
what are the 6 criteria (WHO) for a genetic screening programme?
a) there is an important public health burden in the target population (no. of people affected or severity of problem).
b) the natural history of the disease should be well understood.
c) there is general agreement on the benefits expected from the programme, from the point of view of the professionals, patients and community.
d) a suitable test exists with known predictive value (i.e. risk of disease due to mutations in the screened genes is known).
e) effective interventions exist to reduce morbidity and mortality among susceptible individuals.
f) should be cost effective.
A genetic screening programme should only be considered if the potential benefits to the screened individual clearly outweigh any potential harm.
give examples of population screening programmes?
- Newborn blood spot (NBS) screening programme - heel prick for 9 conditions at 5 days old. only Conditions that can be treated/better managed by early intervention & treatment available. sufficient sensitivity and specificity.
- FASP - first trimester combined scan (mat age, 2 biomarkers, NT + scan), second trimester quadruple scan (4 biomarkers and mat age) for T21 only + more detailed scan at 18 weeks
Detailed ultrasound scan during pregnancy, looking in detail at fetal anatomy. Fetal abnormalities are associated with chromosomal abnormalities and invasive Cytogenetic testing is offered. Micorarray can be offered if One or more structural abnormalities or NT >3.5mm
- Down Syndrome Screening Programme - biomarkers . risk >1:150 = invasive cytogenetic testing. Now includes NIPT (non-invasive). also NIPD and x-linked fetal sexing
what are advantages of genetic screening?
- PST - provide interventions and treatment
- identify at-risk family members
- may prevent illness and death
- psychological preparation
- avoidance of environmental factors eg. medications
- Detection of carrier status can enable individuals to make informed reproductive or lifestyle decisions.
what are disadvantages of genetic screening?
- costly
- false negs and positives
- false reassurance if negative
- informed consent eg. newborn screening
- carrier status for proband and family
- violation of privacy - may be obliged to tell family
- anxiety - especially if reduced penetrance
- pressure to make reproductive choice or take test
- stigma
- employability/insurance
- negative eugenics
- equity
- vus
what is the most common female chromosomal abnormality and why are only 10% of cases diagnosed? name two symptoms. what is the cause? what is recurrence risk?
XXX triple X may also be mosaic eg. 47,XXX/46,XX or 45,X/47,XXX
can be normal
tall may have primary amenhorrea
most commonly occurs as a result of nondisjunction during meiosis, although postzygotic nondisjunction occurs in approximately 20% of cases.
(<1%) - meioses mostly produce eggs with one X
what are features of Tetrasomy X (48,XXXX)?
tall, low IQ, reduced fertility
how are sex chromosome aneuploidies identified?
prenatal = QF-PCR+karyotype
postnatal = karyotype - shows structural abnormality and recurrence risk. usually referred due to infertility
what is sex determination?
the process that determines the biological sex of an offspring and as a result the sexual characteristics that they will develop
what is the role of the SRY gene in male sex determination Yp11.2?
Sex Determining Region Y (SRY) protein and expression initiates molecular processes for male development and determination. when absent, ovaries develop.
SRY is thought to induce SOX9 gene expression, which in turn induces Sertoli cell differentiation resulting in testis formation and androgen production
SRY also downregulates or supresses the female sex-determining pathway
how does sex determination occur in females?
During female development, the Wnt4 and Foxl2 genes are expressed and result in upregulation of downstream female genes. This pathway results into the differentiation of granulosa cells and theca cells, oocyte production and ovarian follicle formation.
