Prenatal Testing in the Genomic Era Flashcards
AMA cutoff reasoning
- equal risk of miscarriage and risk for affected pregnancy
- cost of testing in any woman over 35y thought to be offset by savings of not having affected babies
low AFP
-increased risk for DS
abnormal serum screen
warrants offering of amniocentesis
factors influencing changes to ACOG guidelines
- importance of patient autonomy
- improvements in sensitivity of first and second trimester screening
- reduced risk of miscarriage by use of ultrasound in diagnostic procedures
MPSS
- all cfDNA extracted from maternal serum sample is sequenced
- precise molecular counting allows for determination of fetal aneuploidy
targeted sequencing
focused on certain aneuploidies by only studying specific sequences
SNP NIPS
- analysis of SNPs to determine genotype and relative copy number for each chromosome of interest
- differentiates between maternal and placental DNA
ACOG 545
-released May 2012
-recommended NIPS for:
+women 35+
+suggestive u/s findings
+prior pregnancy with Trisomy
+parental translocation
+positive MSS
PPV
percent of positive results that are truly positive
-affected most by test sensitivity
sex chromosome aneuploidy PPVs
between 20-40%
NPV
percent of negative test results that are truly negative
high maternal BMI
leads to low fetal fraction and increases the risk for no-call result on NIPS
no-call results on cfDNA screens
-can be related to low ff
-increased risk for aneuploidy (~23%)
+offer GC with diagnostic testing
+repeat testing only provides result 50-60% of time
+namely increased risk for triploidy & Tri18 in which placenta is smaller
reasons for false positive results
- CPM
- vanishing twins
- maternal malignancy
- unknown factors
ACOG/SMFM 640
-pretest counseling, RBL
-combined serum &/or NT better than cffDNA for first line testing
+simultaneous first tri screening not recommended
+AFP and/or ultrasound screening recommended in conjunction
-microdeletion cfDNA testing should not be performed routinely
-NIPS should not be used in multiple gestations
ACMG 2016 position statement
-should not be restricted only to high risk women
+however, should not be used routinely
+still recommends use of 2nd tri AFP and 1st tri ultrasounds
ACOG practice bulletin 153
-different screens and tests with RBLs
+importance of informed consent and patient decision-making
prenatal CMA
- per ACOG 162 should be offered whenever an anomaly is seen
- should be offered to any woman undergoing invasive testing
- can identify 6% of cases with an anomaly and normal karyo, 1.7% with abnormal screening and normal karyo
- recommended as part of workup for IUFD
CVS loss rate per ACOG 162
1 in 455
amnio loss rate per ACOG 162
1 in 900
ACMG and UCS
- conditions tested should be serious and patients undergoing it should use it for intent of reproductive decision
- consent to ACMG 56 results (especially adult-onset conditions)
- should only use well-characterized mutations with predictable phenotypes-clinical association
- all labs doing UCS should comply with ACMG best practices
CF carrier screening
- offered to all reproductive age women
- incidence of 1 in 2500, 1 in 25 carrier frequency in caucasian couples, lower in other populations
- panethnic 23 mutation panel sufficient-CFTR gene sequencing IS NOT
- condition overview: med survival age 42y, primarily affects pulmonary, pancreatic & GI function
SMA carrier screening
- variability in genotype-phenotype correlation
- incidence of 1 in 6000-1 in 10000, carrier frequency of 1 in 40-1 in 117
- severe condition overview: characterized by degeneration of spinal cord motor neurons leading to skeletal muscle atrophy
hemoglobinopathy carrier screening
- all patients should have RBC+CBC & a low MCV should prompt further investigation
- hemoglobinelec ethnicity based with known increased risk for Hgb-opathies in certain ethnicities
- normal heme-elec should still be followed-up to rule out alpha-thal
low MCV
below 80
ethnicities with know hemoglobinopathy risk
African, Middle Eastern, West Indian, Southeast Asian & Mediterranean
AJ condition carrier screening
- always: Canavan, Tay-Sachs, CF, familial dysautonomia
- new: bloom syndrome, familial hyperinsulinism, FA, Gaucher, GSDs, Joubert syndrome, MSUD, MPS-IV, Niemann-Pick, Usher
ACOG #690
-gives guidelines for what is an appropriate panel of universal carrier screening
+carrier frequency of 1 in 100 or greater
+well-defined phenotype
+condition would have a detrimental effect on QoL causing ID, DD, handicap, require medical or surgical intervention and have effects early in life
+be able to be diagnosed prenatally and have possible interventions for treatment or delivery that could improve outcomes
+should primarily not include adult-onset conditions
elements of pretest counseling for ECS
- outcomes can’t always be predicted by conditions screened-phenotypes not always well-defined and detection for rare conditions might not be great
- screen-negative results reduce but do not eliminate residual risk
- panels will change over time, but re-testing is not recommended
needs and future directions with ECS
-prospective studies to compare ECS to ethnic-based carrier screening
+patient and provider attitudes
+outcomes-better for children?
-cost-effectiveness studies
-educational tools and decision-making aids for patients
CFTR I148T allele
- used to be included in pan ethnic 25 mutation panel and had to be removed b/c it was leading to unnecessary diagnostic procedures
- found more frequently than expected and only disease causing with rarer 3119del6 mutation
five elements of informed consent
- competency
- amount and accuracy of information
- understanding
- voluntariness
- authorization
competency in informed consent
can a decision be made based on an understanding of the consequences of the decision
extrapolating women’s reactions to prenatal microarray results
- ability to have info felt like an offer that was too good to pass up
- blindsided/unprepared for abnormal results
- uncertainty & unquantifiable risks
- need for support
- toxic knowledge-wanting to close Pandora’s box
sensitivity
ability to detect true positives
specificity
ability to identify those who do not have the disease correctly
serum markers
-surrogate markers-not directly related to chromosomal anomaly
+AFP-produced by fetus
+uE3, inhibin, beta-hCG placental
-reported as MoMs to allow more easily explainable results for clinicians, consistency and correction for differences between labs
detection rate
- sensitivity
- uses known affected population
- number of correctly identified affected pregnancies
false negative rate
- cases of known affected missed by test
- 100-sensitivity
specificity
- population of unaffected
- how often do we correctly identify unaffected cases
false positive rate
- 100-specificity
- cases of known unaffected incorrectly identified
First tri screen
-MSS analyses \+hCG \+PAPP-A \+inhibin-not always included -NT
second tri screen
*only analytes
-AFP
-uE3
-hCG
+ICT-type of hCG tested by one lab
-inhibin
combined/integrated screen
- NT at 10-14w
- 1st & second tri blood draws
- results only given after 2nd set of results
- better detection rate, but slower timeline
contingent screen
-NT at 10-14w
-first tri MSS drawn and reported
-second tri MSS only run for intermediate risk
+high risk have diagnostic option
+low risk (~ < 1 in 2000) receive no part two test
sequential screen
- NT at 10-14w
- first tri MSS drawn
- second tri MSS drawn
- get part 1 and 2 results
uE3 and AFP over time
increase during pregnancy
inhibin over time
generally constant throughout pregnancy
hCG
decreases during pregnancy
DS analytes
1st tri -low PAPP-A -high hCG -large NT 2nd tri -low uE3 -low AFP -high hCG -high inhibin *greater extremes increase risk
Tri 18 & Tri 13 analytes
1st tri -large NT -low PAPP-A -low hCG 2nd tri -all analytes low
FASTER trial results
with cut-offs of 1:150 with 1st tri and 1:300 for 2nd tri, sequential had a higher detection rate (94%) than 1st tri at different cutoffs and 2nd tri alone
+higher false positive rate
cystic hygroma
protruding sac at the back of baby’s neck, indicative of anomaly-sometimes excluded from screening studies because already high risk
triple vs quad
added analyte reduces inaccuracy, but increases false positive rate
WGS NIPS
- used combination of haplotypes to determine results
- essentially a trio
- we are going to get results we don’t yet know how to interpret it
NT cut-off
generally larger than 3.0 mm considered high risk
large NT associations
- increased risk for Tri 13, 18, 21, Turner
- can indicated other structural anomalies, especially cardiac (10%)
- other single gene conditions (Noonan, multiple pterygium, skeletal dysplasia)
non-chromosomal causes of analyte abnormality
-placental insufficiency and abnormalities
+confers increased risk for miscarriage, IUGR, stillbirth, infant death
-identifies higher risk of maternal hypertension, pre-eclampsia and risk of antepartum hemorrhage
-single gene conditions
low uE3 levels
associated with SLOS, X-linked (harlequin) ichthyosis
high AFP levels
- wrong dates
- multiples pregnancy
- ONTDs, abdominal wall defects
- high risk obstetrical outcomes
- maternal malignancy-VERY HIGH levels
ACHE
processes acetylcholine in neurons, should only be in CSF, so presence in amniotic fluid increases risk of ONTD
ethnicity-based CS model
limited to a certain group of people because of a high risk for particular genetic conditions
population-based CS model
screening for common conditions offered to all individuals
pan-ethnic-based CS model
larger than population based-screening because it targets more than common conditions
reasons for increased AR condition risk
- founder effect
- societal inbreeding over time or due to geographic isolation and consanguinity
- selective advantage
ethnicity melting pot
mixing of ethnicities makes a population-based model of carrier screening challenging
genotyping array platforms
- finite number of mutations
- variable detection rate by disease and ethnicity
- should be used in population carrier screening set-up
sequencing platforms
-uses NGS technology
-increases the number of variants identified
+do we report all of these if unknown effect?
-theorized higher detection across all populations-still limited in practice
-could use in population screening set-up or when one partner is an identified carrier
overall risk to be a carrier of a genetic condition
approximately 1 in 5
MPSS limitations
- struggles when regions are GC rich, such as with chr 13
- cannot distinguish between maternal and fetal cfDNA
SNP NIPS limitations
- cannot he used in multiples pregnancies
- due to failure of maternal & fetal DNA to match, can’t be used in pregnancies conceived with egg donors, consanguinity or when mom has had a BMT or organ transplant
Limitations of NIPS testing
-studies show at least 16% chromosomal anomalies are missed by this analysis alone (does not include CMA mutations)
-not diagnostic, screening
+mesynchamal core more representative than trophoblastic material measured
-risk for discordant results and no-call result
-low incidence conditions difficult to pickup, PPV low
CPM
- can result from abnormal segregation of chromosomes during mitosis or from trisomy rescue
- can cause result discordance, as most of the time abnormality is confined to the placenta
T13 and Turner on CVS
- higher risk for CPM
- consider amnio in place of or in addition
Co-twin demise/vanishing twin and NIPS
-in one study 27% all multiples spontaneously reduced in less than 7w
-contribution of this in discordance is unclear
+aneuploid fetuses are more likely to demise
-additional DNA can remain in maternal blood for ____w (at least 2w)
Maternal obesity & NIPS
-remodeling of adipose tissue in pregnant women with obesity results in increased release of cfDNA of maternal origin
-circulating concentration of fetal cfDNA doesn’t change, but fraction is reduced
+can be seen in women >170lbs
*testing should not be completed until 14w if maternal BMI is >40
High fetal fraction
Could indicate faster placental death
+often seen in DS
Maternal malignancy & NIPS
-Possible outcome that can be identified besides CPM or true aneuploidy
+very abnormal results seen-especially concerning if two chromosomes look funky
-incidence of ~1 in 1000
Maternal mosaicism and NIPS
Higher risk of Turner (possibly other sex chromosome aneuploidies too) result on NIPS
+related to mosaicism with increasing maternal age
No-call results on NIPS
could be related to:
- failed quality metrics
- low FF
- fetal aneuploidy (2.5x more likely)
CVS
-Diagnostic procedure typically done between 11-13w
+increased miscarriage risk before 9w
+culture fails more after 13w
-transcervical v transabdominal depends on location of placenta, fetus number & provider comfort level
CVS complications
- risk for SAB May be slightly elevated
- learning curve for providers
- oromandibular limb hypogenesis in fetuses less than 9w
- club foot
- mosaicism
- infection and/or leakage in <0.5% of cases
Placenta decidua
- normal
- placenta attached to uterus until labor when it separated due to contractions
Placenta accreta
- abnormal
- placenta is attached too deeply to uterus
Placenta increta
- abnormal
- placenta is more deeply attached to the muscle wall around the uterus
Placenta perceta
- abnormal
- placenta grows through uterus and can extend to nearby organs
Immune hydrops
- Rh negative mother produces anti-D Ab (or k mother with K child, etc)
- risk for fetal and maternal blood to mix high during delivery, amnio, CVS
- can increase the risk for anemia in future pregnancies if Rhogam is not administered
MCA Doppler
Measures velocity at which blood is being shunted to fetal brain
-higher number means a sicker baby
invasive prenatal testing advances
-used to be standard karyotype and FISH
-now can use CMA
+detects 6% of anomalies with ultrasound finding, but normal karyo
+picks up diagnosis with 13% of MCA cases
-NGS panels
+can help diagnose Noonan, holoprosencephaly, skeletal dysplasia
-WES & WGS on research basis
+NTD & GU defects have had the largest findings at columbia
limitations of prenatal WES and WGS
-cost \+expensive, insurance often won't cover -TAT \+findings usually identified late then results can take months sometimes -secondary findings \+ACMG 56 -who "owns" and receives this information -future discrimination
