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137 Cards in this Set

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In meiosis 1, do homologs separate or do sister chromatids separate?

Does nondisjunction cause isodisomy or heterodisomy?
homologs separate

nondisjunction causes heterodisomy
In meiosis 2, do homologs separate or do sister chromatids separate?

Does nondisjunction cause isodisomy or heterodisomy?
sister chromatids separate

nondisjunction causes isodisomy
Which gender and stage of meiosis is the most frequent source of trisomy?
maternal meiosis 1, causing heterodisomy
Down syndrome etiologies and frequencies
trisomy 21 (95%)
unbalanced robertsonian t (3-4%) - most often der (14;21)(q10;q10)
mosaic (1%)

recurrence risks for carriers of rob(14;21)(q10;q10):
-males 5%
-females 10-15%
Trisomy 13 (Patau syn) etiologies and frequencies.
trisomy 13 (80%)
+13, rob(13;14)(q10;q10) (20%) - inherited from carrier parent 50% of time, most common translocation in general population, empiric risk of trisomy 13 is 1% per pregnancy from a carrier parent
In which stage of meiosis does crossing over occur?
prophase 1 - pachytene
In which stage of meiosis does the oocyte arrest?
prophase 1 - diplotene - dictyotene
which type of DNA and what areas are stained dark in c-banding?
constitutive heterochromatic

1q, 9q, 16q, Yq, all near centromere and telomere

c-banding is used to determine if a deleted or duplicated region is expressed or not.
What are the risks of an abnormal outcome for de novo
-robertsonian translocation
-reciprocal translocation
3,6,9 rule for de novo rearrangments
robertsonian - 3%
reciprocal - 6%
inversion - 9%
Philadelphia chromosome
BCR-ABL fusion, leads to increased ABL function, promotes growth and differentiation
90-95% of CML cases
translocation in Burkitt lymphoma
translocates MYC proto-oncogene near IHC locus, increases expression
Most aneuploidy is from maternal meiosis 1, what are the exceptions?
Trisomy 16 is 100% maternal in origin (vs. mostly)
XXY is 45% paternal, 55% maternal
45, X is 80% paternal, 20% maternal
Which chromosomes have a UPD phenotype and what is it?
matUPD7 - 10% of russel-silver
patUPD11 - BWS
matUPD14 - dev'l delay, short stature, precocious puberty, scoliosis
patUPD14 - polyhydramnios, low birth wt, severe MR, anomalies
matUPD15 - PWS
patUPD15 - angelman syn
matUPD20 - rare, growth retardation, ?cryptic trisomy 20
matUPD2 (only a few cases reported, IUGR, oligohydroamnios)
matUPD6 (a few cases, transient neonatal diabetes and low birth wt)
matUPD16 - IUGR, normal dev't
What proportion of triploidy is diandric? digynic? What's the phenotype of each? Common features?
85% dyandric
-haploid egg + 2 sperm
-haploid egg + diploid sperm
-pheno: large placenta w appearance of partial mole, usually don't make it to term
15% digynic
-1 sperm + diploid egg
-growth retarded fetus, small and fibrotic placenta, can survive to term

features common to both: 3-4 syndactyly
chromsome abnormalities in spontaneous abortions?
of those with chromosome abnormalities:
20% 45,X
16% triploidy
16% trisomy 16
which trisomy is never seen in blood?

also tetrasomy 12p (pallister-killian),
which segregation of reciprocal translocations is most common and produces balanced or normal gametes?
which segregation of reciprocal translocations follows normal centromere segregation and creates unbalanced gametes?
adjacent 1
which segregation of reciprocal translocations is rare, involves identical centromeres segregating to the same pole, and produces unbalanced gametes?
adjacent 2
what are the two recurring reciprocal translocations and their phenotypes when unbalanced?
usually inherited, not de novo
3% risk of liveborn abnormal for males
5-7% risk of liveborn abnormal for females

similar phenotype to wolf-hirschorn b/c unbalanced offspring have der(4) wit partial monosomy 4p and partial trisomy 8p.
what proportion of inversions are inherited?
pericentric inversions have a greater risk for a liveborn abnormal phenotype if?
the more distal the breakpoints, b/c if a crossover occurs the resulting duplication or deletion is likely to be small enough to be viable (vs. larger dup or del that would lead to infertility or miscarriages)
empiric risk of abnormal liveborn outcome with a pericentric inversion?
10-15%, with small distal segments
empiric risk of abnormal liveborn outcome with paracentric inversion?
supernumerary marker chromosomes?
80% de novo, 20% familial
80% from acrocentrics, 40% from 15
if de novo - abnl pheno 13-16% of time, higher risk if nonacrocentric
what increased cancer risk are these cytogenetic abnormalities associated with?
(mosaic) trisomy 8
down syndrome
1p13, 11p15
(mosaic) trisomy 8 - CML, AML
down syndrome - acute leukemia
47,XXY - breast ca
45,X/46,XY - gonadoblastoma
5q21-22 - colon cancer
11p13, 11p15 - wilms tumor
13q14.2 - RB
what region of Y has microdeletions in non-obstructive azospermia or oligozoospermia? what proportion of cases?
Yq11.2 (AZF region)
8-15% of men with azoo- or oligozoospermia have microdeletions in this region
Turner syndrome etiologies and frequencies
50% - non-mosaic 45,X
20% - mosaic 45,X/normal
-25% 45,X/46,XY - risk of gonadoblastoma
-but note, 95% of prenatally dected 45,X/46,XY mosaics have normal male phenotype
18% - 46,X,i(X)(q10) - the isochromosome is preferentially inactivated
6% ring X with XIST (if no XIST have more phenotype abnormalities b/c both ring and normal X are active)
what is the most common robertsonian translocation?
Types of mosaicism from CVS? i.e. define type 1,2,3
type 1 - direct prep only, from cytotrophoblast, outer later of placenta, less likely to be representative of fetus
type 2 - in cultured prep only - from mesenchymal core, more internal layer of placenta, more like fetus
type 3 - in both direct and cultured prep
levels of mosaicism (CVS and amnio)
level I - single abnormal cell
level II - multiple abnl cells in one culture
level III - true mosaicism - seen in two or more independent cultures - follow-up testing needed
in what proportion of CVS procedures is mosaicism seen? what proportion of those are true fetal mosaicism?
1-2% of CVS has confined placental mosaicism
10% of cases of confined placental mosaicism are associated with true fetal mosaicism
Which chromosomes, when seen as trisomic on CVS are more likely to be mitotic in origin and therefore not an issue for UPD or trisomy in fetus?
2, 7, 8, 10, 12
Which chromosomes, when seen as trisomic on CVS are more likely to be meiotic in origin and therefore have a risk for UPD and trisomy?
9, 16, 22
UPD a risk in what situations?
trisomy mosaicism
roberstonian translocations (most are isochromosomes!)
reciprocal translocations (rare)
pericentric inversion, maternally inherited
ring with chromosome 18 centromer, material distal to p11 and q22 is missing
terminal deletion of short arm of chromosome 5 starting at p13
what is the correct nomenclature for a 14 21 robertsonian translocation?
what proportion of homologous robertsonians are isochromosomes? what is the risk of UPD?
90% of homologous robertsonians are isochromosomes
if homologous, risk for UPD 66-73%
if 14 or 15 involved, test for UPD
what is meiotic drive?
female carriers of balanced robertsonian translocations preferentially segregate the balanced form of the translocation.

evidence: instead of normal offspring have a ratio of 50:50 carriers: normal, it's 60:40.
what proportion of reciprocal translocations is inherited?
What proportion of large structural rearrangements are paternal in origin?
75% of large structural rearrangements are paternal in origin (de novo? from online review course, not specified)

But 90% of de novo non-homologous robertsonians are maternal.
How does the size of the exchanged segments in a reciprocal translocation affect the risk of an abnormal outcome?
small distal segements lead to small imbalances that are more likely to be viable and thus high risk for abnormal phenotype.

large distal segments lead ot large imbalances and low risks for liveborn abnormal but high risks for infertility and miscarriages.
when to test for UPD (ACMG 2001)?
fetuses with level II or III mosaicism on CVS or level II mosaicism on amnio for chromosome 6,7,11,14,15.

fetuses with robertsonian translocation or possible isochromosome involving 14 or 15 - both familial and de novo
children with abnormal phenotype and robertsonian translocation of 14 or 15
suspected UPD dx (neonatal diabetes, russel-silver, bws, etc.)
most inherited rings are from the mother or father?
what proportion of small supernumerary rings are familial?
44% of prenatal cases
13% of postnatal cases (ascertainment bias)
what proportion of small supernumerary rings have an abnormal phenotype?
30% of prenatal cases
75% of postnatal cases (ascertainment bias)
what are the common recurring supernumary marker chromosomes and their phenotypes?
inv dup(15)
22q - cat eye syndrome
i(12p) - pallister-killian
male with a terminal deletion. all material distal to p13 is missing.
female with interstitial deletion of bands q11 to q21.
female with a pericentric inversion on chromosome 4 with breakpoints at p15 and q13, inherited from mother.
46,XY,inv(13)(q13q32)de novo
male with a paracentric inversion on chromosome 13 with breakpoints q13 and q32, not carried by either parent.
female with one normal 18 and one ring 8, with breakpoints at p11 and q22. patient is monosomic for material distal to p11 and q22.
male with a balanced reciprocal translocation between 2 and 8. material distal to 2p13 and 8q12 has been exchanged.
female with an unbalanced reciprocal translocation between 2 and 18, inherited from her father. she has two normal 8s, one normal 2 and a derivative 2. She is monosomic for chromosome 2, distal to p13, and trisomic for chromosome 8 distal to q12.
female with a balanced robertsonian translocation involving 13 and 14.

this is the most common robertsonian translocation and the cause of 20% of cases of trisomy 3 (when unbalanced)
female with trisomy 13 due to an unbalanced robertsonian translocation inherited from her mother.
which stage of meiosis is the reduction division?
meiosis I
2n-> 1n
dipload -> haploid
gender differences in recomb'n
recomb'n F>M overall
both F&M, recomb'n increases near telomeres, but M>F
both F&M, recomb'n decreases near centromeres
what testing do to determine which stage of meiosis non-disjunction occurred?
use a polymorphic marker near the centromere (b/c crossing over less likely) - if MI they will be same as parent (het), if MII they will be same as only one of the parent's alleles (homozygous)

if distal markers used have to take recomb'n into consideration.
most anueoploidy originates in maternal MI, what are the exceptions?
tri 18 - 69% maternal MII
tri 16 - 100% maternal MI
XXY - 54% mat, 46% pat
X - 30% mat, 70% pat
what proportion of triploidy that is paternal in origin?
phenotype of paternal triploidy?
large placenta
small fetus
partial hydatiform mole
heart defect
phenotype of maternal triploidy
small placenta
good fetal devel't
early loss
Giemsa staining after trypsin treatment

AT rich stain dark (G+) - few genes
GC rich stain light (G-) - most genes
quinacrine fluorescence dye

AT rich stain positive (flour. brightly)
GC rich stain negative (flour. weakly)
'reverse' banding

opposite of G and Q banding. Use to highlight telomeric regions
Constitutive heterochromatin stains dark, euchromatin stains light
poymorphic regions of human karyotype
-acrocentric stalks and satellites
-pericentromeric regions of 1, 9, 16 (amount of heterochromatin). large variants referred to as 1qh+, 9qh+, etc.
-long arm of Y chromosome is highly polymorphic
cytogenetic nomenclature
additional material of unknown origin
cytogenetic nomenclature
dicentric chromosome
cytogenetic nomenclature
cytogenetic nomenclature
x-autosome balanced translocation, which X is inactive?
always the normal X, so as to preserve the autosome balance.
what is the theoretical vs. empirical risk of an unbalanced offspring (gamete?) from a carrier of a balanced reciprocal translocation?
50%, theoretical (b/c 50% alternate and 50% adjacent 1 segregation)

but empircal is 10-15%
are robertsonians usually monocentric or dicentric?
cytogenetic causes of 1st trimester SAB?
50-60% of 1st tri SAB have abnl chrom
-50% autosomal tris (tri 16 most common)
-25% 45,X (99% abort)
-20% triploid, tetraplid
-5% structural abnlts
about how many genes escape x inactivation and where are they?
on Xp

explains why i(Xq) causes Turner syndrome and why X aneuploidies have abnormal phenotypes?
where is the x inactivation center?
which X is XIST (x inactivation specific transcript) expressed from?
what does the XIST transcript do?
X inactivation center is at Xq13

XIST is expressed from the inactive X only

XIST RNA remains in nucleus, coats inactive X
cytogenetics of male infertility
-2-5% (oligospermia),15% (azoosp.) of infertile men ahve chromosome abnlts
-47,XXY is most common cytogenetic cause of azoospermia
-virtually all translocations involving x or y produce infertile males
-submicroscopy Yq dels - 12% of nonobstructive azoosp
cytogenetics of female infertility
many carriers of balanced X;autosome translocations are infertile, esp. if breakpoint is between q13 and q26 ('critical region' for ovarian fxn)
resolution of metaphase banding (500 bands)?
50 genes, 6Mb
resolution of prometaphase banding (1000 bands)?
25 genes, 3Mb
FISH resolution?
1 gene, 1-100kb
aCGH/PCR/MLPA resolution?
1 gene, <1-100kb
PCR use for:
-bal'd rearr't
-bkpt detect.
-parental origin
-dosage - good, best w/ polymorph
-bal'd rearr't - can't do
-bkpt detect. - good
-parental origin - only w/ polymorph
-UPD - only w/ polymorph
-bal'd rearr't
-bkpt detect.
-parental origin
-dosage - good
-bal'd rearr't - good
-bkpt detect. - good
-parental origin - can't do
-UPD - can't do
-bal'd rearr't
-bkpt detect.
-parental origin
-dosage - good
-bal'd rearr't - can't do
-bkpt detect. - can't do (?)
-parental origin - can't do
-UPD - can't do (but SNP array can!)
different types of FISH probes and their use?
-painting probes - delineate whoel chromosomes, useful for translocations, identifying derivative chromosomes
-repetitive probes - (eg. alpha satellites at centromeres). good for ID'ing marker chromosomes and for interphase analysis for aneuploidy
-unique sequence probe - use for microdel/dup, telomeres
normal copy number variation?
11-12 loci polymorphic/individual
length: mean 500kb, median 200kb, range 150kb-2Mb
imprinting definition
An epigenetic, gamete-of-origin modification of the
genome which results in monoallelic gene expression
and allele-specific DNA methylation (usually of the silent
or inactivated allele).
imprinting details - time, tissue
-tissue-specific (may be imprinted in some tissues, biallelic in others)
-developmentally regulated (i.e. imprinted early in dev't but biallelic in adults)
chromosomes with known imprinting
1,5,6 (TNDM),7(RS),11(RS, BWS),12,13,14,15(PWS,AS),18,19,20,X
triploidy with diandry vs. digyny?
diandry - large cystic placenta, little or no fetus, dispermy most common mechanism,

digyny - underdev'd placenta, relatively 'good' embryonic dev't, early SAB

diandry > common than digyny
markers as indicators of MI vs. MII non-disjunction?
MI NDJ - centromeric markers are heterozygous, distal makers heter or homo (recomb'n)

MII NDJ - centromeric markers homozygous, distal makers homo or hetero (recomb'n)

if ALL markers are homozygous, i.e. complete isodisomy - likely monosomy rescue
pat UPD6
transient neonatal diabetes
severe IUGR
sometimes - macroglossia, umbilical and inguinal hernias
mat UPD7
pre and postnatal growth retard'n
7-10% of pt with russel-silver
pat UPD11
10-20% of BWS pt
only affects distal 11p (somatic crossing over?)
mat UPD14
IUGR, short stature, small hands and feet
precocious puberty
pat UPD14
characteristic facies
severe neuro involv't
skeletal anomalies - small thorax, abnl ribs, short limbs
growth retard'n
mat UPD15
20-25% of PWS
ass'd with AMA
most cases heterodisomy (MI)
pat UPD15
<5% angelman synd
most cases isodisomy (monosomy rescue)
AMA ass'n
Williams syndrome
microdel/contiguous gene synd.
-MR w/ microcephaly
-**friendly, loquacious; hoarse voice; *hyperacusis
-dysmorph: fullness around eyes and lips; medial eyebrow flare; depressed nasal bridge, epicanthal folds; irises blue w stellate pattern; long philtrum
-transient infantile hypercalemia
-supravaluvular aortic stenosis, PS, PPS, VSD, ASD
-short stature - pre and/or postnatal
-connective tissue dys
-tests: del(2)(q11.23) detectable by FISH in >90% of pt; 3Mb del - most NOT cytogenetically detectable
-wilms tumor (50%)
-aniridia - cataracts, nystagmus, ptosis
-MR, microcephaly
-short stature
-cryptorchidism, hypospadias, renal cysts, VSD
-del11p13 in >90% be cytogenetics or molecular methods
-abdominal wall defetcs
-increased risk embryonal tumors
-85% sporadic, 15% familial
-50-60% abnl meth'n LIT1/KCNQ1OT1
-10-20% paternal UPD11p (often mosaic - hemihypertrophy)
-2-7% abnl meth'n H19
-5-10% sporadic, 40% familial - mtn CDKN1C
-1% pat dup 11p15
-1% mat transloc'n
Angelman synd.
-postnatal microcephaly, flat occiput
-severe MR, little/no speech
-ataxia, arms held horizontal; seizures
-unprovoked laughter, happy affect
-wide mouth, protruding tongue, prominent mandible
-del(15)(q11-13) 70% (fair complexion/hair)
-UBE3 mtn 15-20% (?)
-UPD15pat <5% (mostly monosomy rescue)
-imprinting mtn 5%
Miller-Dieker syndrome
-lissenceph., type 1 - complete agyria or w/ limited pachygyria
-severe MR, spasticity, seizures
-microcephaly, bitemporal narrowing, vertical furrows on forehead, prom't forehead, short nose, upturned nares, protuberant upper lip, thin vermillion border, small jaw
-tests: del(17)p13.3 including LIS1 - 50% by cytogenetics, 100% by FISH
-for isolated lisenc. sequence - normal karyotype, del by FISH in 30-40%, point mtn in LIS1 in 40%
smith-magenis syndrome (SMS)
-MR, hyperactive, destructive, self-abusive, self-hugging, polyembolokoilamania (inserting foregin objects), onychotillomania (picking nails), pain insensitivity
-sleep disturbance
-dysmorph: brachycephaly, flat face, arched eyebrows, epicanthal folds, prominent mandible, cleft palate, hoarse deep voice, brachydactyly, short stature
-heart defect
tests: ~90% del(17)(p11.2)- most cytogenetically visible, but confirm by FISH or array
-5-10% - mtn in RAI1
which deletion syndromes have deletions that are cytogenetically detectable in the majority of cases?
most are NOT cytogenetically detectable and need FISH or array.

-most of SMS del(17)(p11.2) are cytogenetically detectable, but you still need to confirm by FISH. deletion is 4Mb, one of the biggest.
-the larger deletion syndromes:
--cri du chat del(5p)
--wolf-hirschhorn del(4p) (60-70% detectable)
--jacobsen del(11q)
--18p-, 18q-
which is the most common microdeletion syndrome?
22q11.2 (1/4000)

vs. others due to flanking LCRs (WS, AS, PWS, SMS, Sotos) ~1/10,00-1/20,000

vs. larger dels not due to flanking repeats (cri du chat, wolf-hirs., MDS, RB, WAGR) ~1/50,000-1/100,000
chromosomal composition of complete hydatiform moles?
ovarian teratomas?
partial hydatiform moles?
complete mole - 46, all paternal
ovar'n teratoma - 46, all maternal
partial mole - 69, most often 2 paternal compliments due to dispermy
A female patient with severe mental retardation, short stature, and other malformations has a
karyotype of 45,X/46,X,r(X).
-pheno due to failure of X inactivation
-lack of expression of XIST
-both normal and ring X are active
-XIST gene often deleted on ring X (more often than not)
phenotypes with a ring X? what does it depend on?
larger ring X, with XIST: Turner syndrome (6% of cases), usually mosaic

small ring X, without XIST: more severe phenotype - MR, syndactyly
female with one normal X and one abnormal X as part of an unbalanced rearrangement - which X is inactive?
preferential inactivation of the abnormal X
females with balanced X-autosome translcoation - which X is inactive?
preferential inactivation of the normal X
risk of abnl child for carriers of
-rob(13q14q) - 1% (tri 13)
-rob(14q21q) - <1% for fathers (tri 21)
what is the cause of sotos syndrome?
microdeletion of 5q including the NSD1 gene or mutation in that gene
cell culture needed for aCGH?
no! can use non-dividing cells, archival samples.
limitations of array CGH?
-can't detect polyploidy (b/c software averages/normalizes across genmoe)
-can only detect mosaicism >20% (and dependent on size of imbalance)
-no info on balanced rearrangements, location of rearranged sequence responsible for imbalance
BAC vs. oligo vs SNP arrays?
BAC - initial clinical arrays, some targeted (like many FISH at once), some whole genome at defined intrevals

oligo - smaller sizes of DNA, more labs moving to this now, higher res'n, can pick up very small imbalance (smaller than BAC), ?how handle polymorphism

SNP - can detect UPD (heterozygosity vs. homo'y), can help clarify artifacts on other chips (b/c if heterozyg, then not a deletion)
what parental cytogenetic abnormalities is seen in children with microdeletion syndromes assocated with flanking LCRs?
inversion polymorphisms!
-28% of transmitting parents of kids with Williams had inv
-67% of transmitting parents of kids with deletion AS had inv
-100% of tranmitting parents of japanese pt with sotos due to deletion
sotos syndrome
NSD1, 5q34 deletions
-frontal bossing, high arched palate, prognathism, pointed chin, large years, overgrowth (hc, ht, wt, with ht and wt returning to normal in childhood)
-mutation or deletion of NSD1 on 5q34
-japanese pt - 52% have del
-non-japanese pt - 6% have del
-discovered with arrays, recently described
-region with multiple complex LCRs - lots of rearrangemnet
-ass'd with inversion polymorphism
-MR, hypotonia and poor feeding in neonatal period, friendly behavior, bran anomalies, distinctive facial features, low birth weight,
pick up on array after normal karyotype?
children with MR
cyto - 5-10% yield
targetted BAC (after normal cyto) - additional 5-6%
oligo array (after normal cyto) - additional 10-12%
current estimates of array yield, without cytogenetics in pt with MR/DD with or without dysmorphic features?
whole genome BAC array 17-19%
100-200k oligo array 20-21%

(additional 10% beyond karyotype - based on meta-analysis)

(likely includes things that would be picked up on karyotype and benign polymorphisms)
what factor in when deciding if a a CNV is benign or pathogenic?
-how big? bigger more likely to be pathogenic (usually)
-reported ass'n with normal or abnormal phenotype
-if present in normal parent - may be benign, or may be ass'd with increased risk (ex. 1q21.1 ass'd with TAR syndrome, often seen in an unaffected parent)
-overlap a clinically significant gene?
CNV in autism?
-de novo CNVs found in 10% of sporadic, 3% with affected FDR, vs. 1% of controls
-16p11.2 (600kb) - del in 1% of pt with autism (vs. 0.01% gen pop), dup also seen in autism
-dup(15)(q11q13)mat - 1-3% of autism/ASD
CNV in neuropsych disease?
alzheimer disease: AD early onset - ~8% have dup(21)(q21) (amyloid precursor protein)

parkinson disease: AD PD dup or trip of 4q21 (alpha-synuclein) locus

shizophrenia: de novo CNV in 10% of sporadic cases vs. 1.3% of controls
prevalence of balanced translocations related to infertility?
-newborn surveys - 0.2%
-habitual SAB couples - 3-4%
->3 consecutive SAB - 9%
-infertile - 0.6%
->10 IVF cycles failed - 3.2%
nuchal lucency>4.0 - % screen negative? what do?
>4.0 - highly unlikely to screen neg; 33% aneuploidy; offer diagnostic testing

3-4 - 8% will screen neg; 17% aneuploidy; offer diagnostic testing
risk of amnio?
likely <1/200
unlikely as low as 1/1200

(problems with FASTER data)
is amnio ass'd with PPROM
1% risk within 48 hrs
BUT 91% survive afterwards
risk of CVS?
0.6-0.8% above amnio
1.0% above background
advantages of PUBS?
-full fetal karyotype in 48 hours
-hematologic and serologic parameters
-assessing mosaicism

-disadv: 1-2% risk of fetal loss, technically more difficult, later in gestation (>18wks)
-cvs - >=10weeks
-amnio - >=15weeks
-PUBS - >=18weeks
does resolution of increased nuchal translucency decrease risk?
no! resolution occurs in both euploid and aneuploid fetuses

-BUT if the risk of an adverse outcome is higher in pregnancies with nuchal edema @ 20wk (vs. not)