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T21

T 18

T21

T 18

Copy Number Variants

T 1345, XO

47, XXY47, XXX

47, XYY

T 1345, XO

47, XXY47, XXX

47, XYY

Diagnostic Procedure

Improved Screening Diagnostic TestingMore Information

Other Chromosome Abnormalites

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Chromosomal Microarray Analysis (CMA)

Karyotype

Resolution:>7-10 Million Base Pairs

(7-10 Mb)

Resolution:< 0.5 Million Base Pairs

(< 500 kb)

Chromosomal Microarray(CMA)

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Microdeletion Syndromes

DiGeorge 22q11 Deletion 3.5Mb

Miller Dieker 17p13.3 deletion

Prader Willi 15q11-13 deletion 4MB

Smith Magenis 17p11.2 deletion 5Mb

Wolf Hirshhorn 4p16.3 deletion 1.9Mb

Williams-Beuren

7q11.23Deletion 1.5Mb

Non-SyndromicMicro Del /Dups

15-20% yield by CMA in children with unexplained developmental delay/ID, and congenital anomalies compared to ~3% with karyotype

16p11.2 Autism 0.55Mb

1q21.1 ID, microcephaly, cardiac, cataracts

0.8Mb

16p13.11 Autism, ID, and schizophrenia

0.8Mb

Velo Cardio Facial Syndroe

Postnatal Studies

Structural Anomalies

Array Adds Significant Clinically Relevant Information in Cases With Normal Karyotype

Structual Anomlay

Fiorentino 6.1 %

Rosenfeld /Shaffer 6.6 %

Schwartz 5.7 %

NICHD 6.0 %

Frequency of CNVs in Single & Multiple Systems Ultrasound Anomalies

Anomaly system n= 752 CNV array findings (n)

Additionalbenefit (%)

SINGLE System 454 25 5.5%MULTIPLE System 298 36 12.1%

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Evaluation of Structural Anomaly Seen on Ultrasound

22q11 DeletionSpectrum of Clinical Features

N =900%

Learning Disabilities-none/mild- 62%-moderate/severe 30%

Cardiac Defects 75%

Genitourinary Defects 36%

Palate Anomalies 76%%-cleft palate 9%-velopharyngeal insufficiency 67%

Abnormal facial features frequent

Growth Delay (<3rd %) 36%

Psychosis /Behavior Problems 25%

Hypoparathyroid 60%

Chromosome 22

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7q11.23 microduplication syndrome

Amniocentesis:Karyotype: 46,XYArray: 1.39 Mb gain in 7q11.23

Van der Aa, et al. Fourteen new cases contribute to the characterization of the 7q11.23 microduplication syndrome. European Journal of Medical Genetics 2009

Should We Offer Microarray To All Pregnant Women

PrimaryStudy

NPathogenic CNVs

Frequency

PrimaryStudy

3060 33 1.1%

Present Study

2199 27 1.2%

Total 5259 60 1.1%

Frequency Of CNVs In Karyotype Normal Cases

Sampled For AMA, Positive Screen, or Anxiety

Normal Ultrasound

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Microdeletion Syndromes with Severe Phenotype

Region PhenotypeFreq. in 31,516 Cases

22q11.2 del ID; schizophrenia (25%) 1 in 167

16p11.2 del ID; autism, other DSMIV (95%) 1 in 241

1q21.1 del ID, schizophrenia 1 in 309

15q13.2-q13.3 del ID, Epilepsy (BP4-BP5) 1 in 358

22q11.2 dup 22q.11.2 duplication syndrome 1 in 384

7q11.23 del Williams syndrome 1 in 415

16p11.2 dup ID, Schizophrenia 1 in 470

15q11.2-q13 dup ID; Autism 1 in 508

15q11.2-q13 del Prader-Willi/Angelman 1 in 553

1q21.1 dup ID, Autism 1 in 584

D. Moreno De Luca et al. Mol Psych 2013

Top 10 Seg Dup-Mediated CNVs Data from Case/Control Analysis

Prenatal Study >100 Different Pathogenic CNVs

del 16p11.2 and Autism

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Non-CarrierMean 108SD 12

16p11.2 Deletion

CarrierMean 80SD 15

Variable Expressivity/Incomplete Penetrance

Advantages of Identifying an Etiology

• Referral to appropriate specialists & social services • Targeted treatment• Identify special education resources• Appropriate surveillance & long term follow up• More accurate recurrence risk estimate• Prenatal diagnosis in subsequent pregnancies• Referral to parent support groups and on-line

resources

As genomic technologies provide testing for a larger spectrum of phenotypes, pregnancy termination is only one

of many uses of the information obtained prenatally

Why Would I Want to Know This?

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So, why aren’t all women asking for whole genome CMA ?

-

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NIPD for Common Trisomys

Trisomy 18 Trisomy 13 Trisomy 21

Detection rate

False positive

Detection rate

False positive

Detection rate

False positive

Sequenom ‐ Lo 84% 2% 44% 6% 100% 2.1%

Sequenom ‐ Lo(GC correct)

92% 2% 100% 1% n/a n/a

Sequenom – Palomaki 100% 0.3% 92% 1% 98.6% 0.2%

Sequenom – Palomaki(GC correct)

100% 0.7% 92% 0.5% 99.1% 0.1%

Verinata – Bianchi* 97% 0% 79% 0% 100% 0%

Verinata – Bianchi (all samples**)

97% 0.6% 81% 0% 100% 1.5%

Ariosa ‐Sparks 98% 0.1% N/A N/A 100% 0.1%

*with the “no call zone”**at z=2.5 cut‐off

Chen et al. (2011), PLoS ONE; Chiu et al. (2011), BMJ; Palomaki GE et al. (2011), Genet. Med; Palomaki GE et al. (2012), Genet. Med.; Bianchi et al. (2012) Obstet Gynecol

cffDNAAn Excellent Screening Test

• Not Diagnostic

• False Negative Results

• False Positive Results

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M

M

MM

1997

F

F

Chromosome 21

Chromosome 1

VV V V

Euploid Trisomy 21

X X

V

Ratio Chromosome 21:1

Euploid Trisomy 21

1:1

X X3:2

10% Fetal DNA/90%MaternalDNA

In Placenta:

In Maternal Circulation

Euploid

1:1

Trisomy 21

1.05:1

Relative Chromosome Dosage (RCD)

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Which Test To Order

Trisomy21 Trisomy 18 45,X No Call

Sens Spec Sens Spec Sens Spec

Counting Approach I >99% 0.1% 99.9% 0.4% 94.4% 0.6% 0.9%

Counting Approach II >99% 0.2% 97.4% 0.4% 95.0% 1.0% 0.9%

Targeted/Array>99% 0.1% >98% <0.1% 91.5% 0% 3.0%

SNP>99% <0.1% 96.4% <0.1% 92.9% <0.1% 5,8%

Combined Screen: Sens 80-85% for 3-5% Screen Positive Rate

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Are They Making an Informed Decision ?

- widespread misconception that all intellectual disability = Down syndrome and

that’s all we can test for…

Data adapted from Wellesley, D, et al., Rare chromosome abnormalities, prevalence and prenatal diagnosis rates from population-based congenital anomaly registers in Europe. Eur J of Hum Gen, 11 January 2012.

Ferguson-Smith, M.A. Prenatal Diag 1984

Maternal Age

Freq of Chrom Abn

% Trisomy 21,18,13

< 35 0.93% 18%

35 1.2% 37%

40 2.1% 68%

45 6.6% 78%

Advanced Maternal Age:Residual Risk for a Cytogenetic Abnormality

after cffDNA

Amniocentesis Performedfor AMA

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Positive First Trimester ScreenResidual Risk for a Karyotype Abnormality after NIPT

State of California Screening Program N= 1,324,607 Screened

Mosaic 186    ( 6.2%)Other Tris 92    (3.1%)Ins/Del 88    (2.9%)Structural 101    (3.3%)Balan 97 (3.2%)Unbal 3    (0.1%)Triploid 29    (1.0%)Marker 9    (0.3%)

Norton: SMFM 2014 

Screen Positive68,990 (5.2%) 

Invasive Testing26,059 (37.7%)

Abnormal2992 (11.5%)

Not Detectable by NIPT504 (16.8%) 

Detectable by NIPT2499  (83.5%) 

For Patients with Positive First Tri ScreenResidual Risk of Chromosome Abnormal after 

Normal NIPT1:52

(Includes Sex Chr 247  (8.2%))

Does Not Include Microdeletions or Duplications

cfDNA FTS

Detection 38/38 (100%)(93.4-100)

30/38 (79.0%)(66.3-100)

p=0.008

FPR 0.06%(9/15050)

5.4%( 854/15050)

p<0.001

PPV 80.8%(67.5-89.6)

3.4%(2.4-4.8)

p<0.001

NPV 100% 99.9% p=0.005

LR+ 1755 14.6

LR- 0 0.22

cfDNA vs FTS for T21N= N – 15,841

Trisomy 21 = 1:417Age 30.7

Maternal Age <35(DS 1:630)

FTS <1/270(DS 1:1870)

Total 11,994 14,957

Sensitivity 100% 100%

Specificity 99.95% 99.95%

PPV 76.0% 50.0%

NPV 100% 100%

LR+ 1996 1869

LR- 0 0

Confidential

cfDNA in Low Risk Patients

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T21

T 18

T21

T 18

Copy Number Variants

T 1345, XO

47, XXY47, XXX

47, XYY

T 1345, XO

47, XXY47, XXX

47, XYY

Diagnostic Procedure

Improved Screening Diagnostic TestingMore Information

Other Chromosome Abnormalites

Counseling Must Change

• At present women undergoing screening only receive limited information about the potential phenotypes that can be diagnosed.

• Patients having NIPT as “replacement “ for invasive testing need counseling describing limitations compared to invasive testing

What Patients Should KnowBasic Information

• Cytogenetic abnormalites occur in approximately 2% of pregnancies• Whole chromosome abnormalities  0.6%• Microdeletions and duplications       1.1 % 

• All cytogenetic abnormalities have clinical consequences varying from mild to severe• Both whole chromsome abnormalites and microdeletions can 

have very severe consequences

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ScreeningMeant to  Identify specific whole chromosome abnormities with high (not perfect) sensitivity

T21 (Down Synd), 18, 13, Sex chromosome

Does not identify all abnormalities:Residual Risk depends on indication

Overall Residual Risk:Whole Chromosome abnormality

Positive Screen: 1:50General Population  1:700

Microdeletion/dup 1:80

What patients Should knowDecision Making

Invasive Testing with CMA 

identifies all whole chromosome abnormities and all microdeletions and duplications

Has a Risk  of Pregnancy Loss:

1:500 to 1:700

Obstetricians ?

First Prenatal Visit Education and counseling

• Scope of care and anticipated schedule of visits. • Expected course of pregnancy. • Counseling regarding specific complications. • Discuss routine lab studies/testing. • Discuss high risk conditions. • Education regarding: Labor and delivery, nutrition, exercise, working, air

travel, routine dental care, tobacco use and smoke exposure, alcohol/drug consumption, over-the-counter medications, pets, etc.

• Practices to promote health maintenance such as use of safety restraints including lap and shoulder belts.

• Assess barriers to care (transportation, child care issues, work schedule). • Encourage maternity program enrollment and prenatal classes. • Encourage and provide influenza vaccination • Family medical history. • Genetic history. • Complete needs assessment. • Preterm labor risk, education and prevention. • Assess for tobacco, alcohol, drug use. • Domestic violence screening. • Screen for depression (current or historical) using a standardized screening tool. 

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GC For all OB PatientsGenetic Counselors Needed

• Deliveries per Year:           4 million

• Prenatal Tests*/year 3 million

• 45 minutes/pt 2.25 million counseling hrs

*screening and diagnostic

@ 2000 hrs/counselor 1125 FTE Prenatal Counselors@ 1000 hrs/counselor 2250 FTE Prenatal Counselors

Mutation

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Severe MicrocephalySevere Microcephaly

Left Foot Right Foot

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Differential Diagnosis• Aase Syndrome• Diamond‐blackfan Syndrome• DOOR Syndrome• Duane‐radial Syndrome (DR Syndrome)• Fanconi Anemia (Pancytopenia‐dysmelia Syndrome)• Fetal Hydantoin Syndrome (Dilantin Embryopathy)• Goodman Syndrome• Holt‐Oram Syndrome• Hypomelanosis Of Ito• IVIC Syndrome• Juberg‐hayward Syndrome• Lacrimo‐auriculo‐dento‐digital Syndrome (LADD Syndrome) (Levy‐hollister Syndrome)• Mesomelic Dysplasia (Werner Type)• Nager Syndrome• Normal Variant : Isolated Anomaly• Poland Syndrome (Pectoral Muscle Aplasia‐syndactyly)• Thalidomide Embryopathy• Townes‐brocks Syndrome• Trichorhinophalangeal Dysplasia Type (Langer Gidieon Syndrome)• Trisomy 13• Trisomy 22• VATER Association

Triphalangeal thumb with Polysyndactyly

• Mutation in SHH gene

• Mutations in the Sonic hedgehog limb enhancer cause limb malformations

Sequencing Analysis

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Prevalence

Common Trisomies (21,18,13) 0.2%

Chromosome Abnormalities Other than Common Trisomies 0.4%

Microdeletons and duplications 1.2%

Mendelian Genetic Disorders 0.4%

Structural Congenital Abnormalities (many de-novo mutations)

3.0%

Prevalence and Etiology of Congenital Abnormalities(It’s Not All Down Syndrome)

Non-invasive sequencing of the fetal genome is likely to be a reality in the not-too-distant future

Tremendous counseling and ethical issues

Uncertain Reassurance

Counseling

Scope Creep

Where Are We Going ?

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CVS: Normal KaryotypeArray: arr 17q12(31464079-33406373)x1

TCF2 deletion

Renal Cysts and Diabetes

Increasing Recognition of Microdeletionsand Duplications