707: Efficient and scalable detection of fetal aneuploidy by Digital ANalysis of Selected Regions...

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705 Polymorphisms of the glucocorticoid receptor gene NR3C1 and the association with birth weight and gestational age at delivery Jennifer Wong 1 , Yula Ma 2 , Luca Lambertini 2 , Andrea Weintraub 3 , Joanne Stone 1 1 Mount Sinai School of Medicine, Maternal Fetal Medicine, New York, NY, 2 Mount Sinai School of Medicine, Department of Preventive Medicine, New York, NY, 3 Mount Sinai School of Medicine, Pediatrics, New York, NY OBJECTIVE: To determine the association of glucocorticoid receptor gene NR3C1 single nucleotide polymorphisms (SNPs) with birth weight and prematurity. STUDY DESIGN: This was a single center, pilot study of 80 umbilical cord blood samples collected prospectively from singleton pregnan- cies. DNA was isolated from each blood sample. SNPs were genotyped by Taqman assay (rs6193, rs6194, rs6195, rs6196, rs6198, rs258751) and sequencing (rs6189, rs6190). Linear regression models were cal- culated for birth weight (BW) and gestational age at delivery (GAd). RESULTS: The rs6195 SNP was not polymorphic in our sample, and was therefore excluded from further statistical analysis. The average BW was 3330g [1930-4660g]. The average GAd was 39.5 weeks [32- 41.6] with only 3 deliveries occurring prior to 37 weeks. The BW linear regression model showed a significant correlation with preterm labor, vaginal delivery, maternal Asian ethnicity, and the rs6196 variant (p0.01; r20.270). The rs6196 GG genotype was associated with a 761g reduction in BW (95% CI 125-1398; p0.02). The GAd linear regression model of gestational age at delivery also showed a signifi- cant correlation with preterm labor, betamethasone administration, neonatal intensive care unit admission, as well as the rs6196 GG ge- notype (p0.01; r20.476). In this regression, the GG genotype was associated with an earlier GAd (95% CI 0.92-0.99; p0.01). None of the other SNPs analyzed showed any significant correlation with ei- ther outcome. CONCLUSION: The GG genotype of the rs6196 SNP of the glucocorti- coid receptor gene NR3C1 is associated with both lower birth weight and earlier gestational age at delivery. These data are consistent with existing scientific literature that correlates this and other SNP pheno- types to lower weight, BMI, waist/hip ratio, and decreased insulin resistance. This glucocorticoid-resistant phenotype may ultimately be protective postnatally among hypercortisolemic premature infants. Given the results from this interim analysis, our investigation will continue with a focus on umbilical cord blood collections from pre- mature infants. 706 False positive Down syndrome screening in women with sickle cell anemia Dena Towner 1 , Anna Kneitel 1 , Roberta Obadia 2 , Laila Morris 1 1 UC Davis Medical Center, Obstetrics & Gynecology, Sacramento, CA, 2 UC Davis School of Medicine, School of Medicine, Sacramento, CA OBJECTIVE: This study seeks to determine whether there is a higher rate of false positive serum screening for Down syndrome in women with sickle cell anemia and, if so, which markers contribute to the false positive screen. STUDY DESIGN: This is a retrospective case-control study. Our subjects were all women with sickle cell anemia who were seen in the UC Davis Obstetrics clinics between 1998 and the present (n 29). We chose as controls women who were seen in Prenatal Diagnosis in the same period and who had a family history of hemoglobinopathy (n 211). Fifteen patients with sickle cell anemia and 114 patients in the control population had a trisomy 21 (T21) serum screen. Using these results, the false positive screening rate in each population was calculated. The average value for each serum analyte was compared between cases and controls using a two sample t-test assuming equal variances. RESULTS: The rate of false positive serum screening for Down syn- drome was 40.0% in patients with sickle cell anemia and 28.1% in the control population, odds ratio, 1.71, 95% confidence interval 0.49- 5.83. The estriol values were significantly lower in cases than controls (0.79 MoM and 0.98 MoM respectively, P value 0.04). In the table we show a trend toward lower AFP values and toward higher hCG and inhibin values in cases compared to controls. The mean age of the control population was significantly higher than the mean age of the cases. CONCLUSION: Although the difference between the false positive T21 serum screen rate in patients with sickle cell anemia and our control population is non-significant, the rate is markedly elevated in sickle cell patients (40%) compared to controls (28%). Since our cases had an average age of 25 years, we would expect a positive serum screen rate of only 2%. The estriol values were significantly lower in cases than controls, and there was a trend toward lower AFP and toward higher hCG and inhibin values in cases. This may suggest that there is placental pathology in sickle cell anemia patients contributing to an elevated false positive screening rate. 707 Efficient and scalable detection of fetal aneuploidy by Digital ANalysis of Selected Regions (DANSR) in cell-free DNA from maternal blood Andrew Sparks 1 , Ken Song 2 , Jacob Zahn 1 , Renee Stokowski 1 , Craig Struble 1 , Eric Wang 1 , Wade Barrett 1 , Celeste McBride 1 , Naiping Shen 1 , Kevin Lee 1 , Jigna Doshi 1 , Jill Garrison 1 , Jay Sandler 1 , Michel Sun 1 , Desiree Hollemon 2 , Patrick Pattee 2 , John Stuelpnagel 1 , Arnold Oliphant 1 1 Tandem Diagnostics, R&D, San Jose, CA, 2 Tandem Diagnostics, Clinical, San Jose, CA OBJECTIVE: Use of massively parallel shotgun sequencing (MPSS) to precisely quantify the chromosomal composition of cell free DNA (cfDNA) from maternal blood has shown promise for non-invasive detection of fetal aneuploidy. Because MPSS involves analysis of DNA from the entire genome, the number of sequencing reads required for aneuploidy detection constrains the efficiency, scalability, and thus, clinical utility of this approach. To address these limitations, we de- veloped and evaluated a novel method, Digital ANalysis of Selected Regions (DANSR(TM)), which uses ligation of locus-specific oligos to produce sequencing template only from selected genomic loci. STUDY DESIGN: Prospective analysis of 405 pregnant women involving a training and validation cohort. RESULTS: We developed DANSR assays for 576 loci on each of chro- mosomes 18 and 21, and used these assays to evaluate cfDNA from 405 pregnant women, including 72 trisomy 21 (T21) and 16 trisomy 18 (T18) pregnancies. Sequencing template from up to 96 patient samples was analyzed in a single flow cell lane on an Illumina HiSeq 2000; 97% of the resulting sequencing reads mapped to expected loci. We trained our aneuploidy detection algorithm on an un-blinded set of 190 normal, 36 T21 and 8 T18 pregnancies. Of the 222 (95%) samples that passed quality control (QC), 35/35 (100%) T21 and 7/7 (100%) T18 samples had chromosome proportion Z-scores 3, and 179/180 (99.4%) normal samples had Z-scores 3. We next per- formed a blinded validation study on an independent set of cfDNA Poster Session V Academic Issues, Antepartum Fetal Assessment, Genetics, Hypertension, Medical-Surgical-Disease www.AJOG.org S314 American Journal of Obstetrics & Gynecology Supplement to JANUARY 2012

Transcript of 707: Efficient and scalable detection of fetal aneuploidy by Digital ANalysis of Selected Regions...

705 Polymorphisms of the glucocorticoid receptorgene NR3C1 and the association with birthweight and gestational age at deliveryJennifer Wong1, Yula Ma2, Luca Lambertini2,Andrea Weintraub3, Joanne Stone1

1Mount Sinai School of Medicine, Maternal Fetal Medicine, New York, NY,2Mount Sinai School of Medicine, Department of Preventive Medicine, NewYork, NY, 3Mount Sinai School of Medicine, Pediatrics, New York, NYOBJECTIVE: To determine the association of glucocorticoid receptorgene NR3C1 single nucleotide polymorphisms (SNPs) with birthweight and prematurity.STUDY DESIGN: This was a single center, pilot study of 80 umbilicalcord blood samples collected prospectively from singleton pregnan-cies. DNA was isolated from each blood sample. SNPs were genotypedby Taqman assay (rs6193, rs6194, rs6195, rs6196, rs6198, rs258751)and sequencing (rs6189, rs6190). Linear regression models were cal-culated for birth weight (BW) and gestational age at delivery (GAd).RESULTS: The rs6195 SNP was not polymorphic in our sample, andwas therefore excluded from further statistical analysis. The averageBW was 3330g [1930-4660g]. The average GAd was 39.5 weeks [32-41.6] with only 3 deliveries occurring prior to 37 weeks. The BW linearregression model showed a significant correlation with preterm labor,vaginal delivery, maternal Asian ethnicity, and the rs6196 variant(p�0.01; r2�0.270). The rs6196 GG genotype was associated with a761g reduction in BW (95% CI 125-1398; p�0.02). The GAd linearregression model of gestational age at delivery also showed a signifi-cant correlation with preterm labor, betamethasone administration,neonatal intensive care unit admission, as well as the rs6196 GG ge-notype (p�0.01; r2�0.476). In this regression, the GG genotype wasassociated with an earlier GAd (95% CI 0.92-0.99; p�0.01). None ofthe other SNPs analyzed showed any significant correlation with ei-ther outcome.CONCLUSION: The GG genotype of the rs6196 SNP of the glucocorti-coid receptor gene NR3C1 is associated with both lower birth weightand earlier gestational age at delivery. These data are consistent withexisting scientific literature that correlates this and other SNP pheno-types to lower weight, BMI, waist/hip ratio, and decreased insulinresistance. This glucocorticoid-resistant phenotype may ultimately beprotective postnatally among hypercortisolemic premature infants.Given the results from this interim analysis, our investigation willcontinue with a focus on umbilical cord blood collections from pre-mature infants.

706 False positive Down syndrome screeningin women with sickle cell anemiaDena Towner1, Anna Kneitel1, Roberta Obadia2, Laila Morris1

1UC Davis Medical Center, Obstetrics & Gynecology, Sacramento, CA,2UC Davis School of Medicine, School of Medicine, Sacramento, CAOBJECTIVE: This study seeks to determine whether there is a higherrate of false positive serum screening for Down syndrome in womenwith sickle cell anemia and, if so, which markers contribute to the falsepositive screen.STUDY DESIGN: This is a retrospective case-control study. Our subjectswere all women with sickle cell anemia who were seen in the UC DavisObstetrics clinics between 1998 and the present (n � 29). We chose ascontrols women who were seen in Prenatal Diagnosis in the sameperiod and who had a family history of hemoglobinopathy (n � 211).Fifteen patients with sickle cell anemia and 114 patients in the controlpopulation had a trisomy 21 (T21) serum screen. Using these results,the false positive screening rate in each population was calculated. Theaverage value for each serum analyte was compared between cases andcontrols using a two sample t-test assuming equal variances.RESULTS: The rate of false positive serum screening for Down syn-drome was 40.0% in patients with sickle cell anemia and 28.1% in thecontrol population, odds ratio, 1.71, 95% confidence interval 0.49-5.83. The estriol values were significantly lower in cases than controls

(0.79 MoM and 0.98 MoM respectively, P value �0.04). In the tablewe show a trend toward lower AFP values and toward higher hCG andinhibin values in cases compared to controls. The mean age of thecontrol population was significantly higher than the mean age of thecases.CONCLUSION: Although the difference between the false positive T21serum screen rate in patients with sickle cell anemia and our controlpopulation is non-significant, the rate is markedly elevated in sicklecell patients (40%) compared to controls (28%). Since our cases hadan average age of 25 years, we would expect a positive serum screenrate of only 2%. The estriol values were significantly lower in casesthan controls, and there was a trend toward lower AFP and towardhigher hCG and inhibin values in cases. This may suggest that there isplacental pathology in sickle cell anemia patients contributing to anelevated false positive screening rate.

707 Efficient and scalable detection of fetal aneuploidyby Digital ANalysis of Selected Regions (DANSR)in cell-free DNA from maternal bloodAndrew Sparks1, Ken Song2, Jacob Zahn1, Renee Stokowski1,Craig Struble1, Eric Wang1, Wade Barrett1, Celeste McBride1,Naiping Shen1, Kevin Lee1, Jigna Doshi1, Jill Garrison1,Jay Sandler1, Michel Sun1, Desiree Hollemon2, PatrickPattee2, John Stuelpnagel1, Arnold Oliphant1

1Tandem Diagnostics, R&D, San Jose, CA, 2TandemDiagnostics, Clinical, San Jose, CAOBJECTIVE: Use of massively parallel shotgun sequencing (MPSS) toprecisely quantify the chromosomal composition of cell free DNA(cfDNA) from maternal blood has shown promise for non-invasivedetection of fetal aneuploidy. Because MPSS involves analysis of DNAfrom the entire genome, the number of sequencing reads required foraneuploidy detection constrains the efficiency, scalability, and thus,clinical utility of this approach. To address these limitations, we de-veloped and evaluated a novel method, Digital ANalysis of SelectedRegions (DANSR(TM)), which uses ligation of locus-specific oligos toproduce sequencing template only from selected genomic loci.STUDY DESIGN: Prospective analysis of 405 pregnant women involvinga training and validation cohort.RESULTS: We developed DANSR assays for 576 loci on each of chro-mosomes 18 and 21, and used these assays to evaluate cfDNA from405 pregnant women, including 72 trisomy 21 (T21) and 16 trisomy18 (T18) pregnancies. Sequencing template from up to 96 patientsamples was analyzed in a single flow cell lane on an Illumina HiSeq2000; 97% of the resulting sequencing reads mapped to expected loci.We trained our aneuploidy detection algorithm on an un-blinded setof 190 normal, 36 T21 and 8 T18 pregnancies. Of the 222 (95%)samples that passed quality control (QC), 35/35 (100%) T21 and 7/7(100%) T18 samples had chromosome proportion Z-scores �3, and179/180 (99.4%) normal samples had Z-scores �3. We next per-formed a blinded validation study on an independent set of cfDNA

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S314 American Journal of Obstetrics & Gynecology Supplement to JANUARY 2012

samples from 171 pregnant women, including 36 T21 and 8 T18 preg-nancies. Only one sample (0.6%) failed to pass QC. All 36 T21 samples(100%) and 8 T18 samples (100%) had Z-scores greater than 3 and allof the 126 normal samples had Z-scores less than 3 (100%). Theseresults were generated from an average of 789K raw sequencing readsper sample, i.e., �5% of the raw reads required for aneuploidy detec-tion using MPSS.CONCLUSION: DANSR represents a high accuracy, cost efficient, scal-able approach to non-invasive detection of fetal aneuploidy.

708 Circulating cell-free fetal DNA for the detection of fetalRHD status and sex: a prospective NAFTNet trial usinga unique approach of reflex fetal identifiersKenneth Moise Jr1, Noemi Boring1, Richard OShaughnessy2,Lynn Simpson3, Honor Wolfe4, Jason Baxter5,William Polzin6, Keith Eddleman7, Daniel Skupski8,Sonia Hassan9, Graham McLennan10, ToniPaladino10, Paul Oeth10, Allan Bombard11

1Baylor College of Medicine, Obstetrics and Gynecology, Houston, TX, 2OhioState University, Obstetrics and Gynecology, Columbus, OH, 3ColumbiaUniversity Medical Center, Obstetrics and Gynecology, New York, NY,4University of North Carolina, Obstetrics and Gynecology; Division ofMaternal-Fetal Medicine, Chapel Hill, NC, 5Thomas Jefferson University,Division of Maternal Fetal Medicine, Department of Obstetrics andGynecology, Philadelphia, PA, 6Good Samaritan Hospital, Obstetrics andGynecology, Cincinnati, OH, 7Mount Sinai School of Medicine, MaternalFetal Medicine, New York, NY, 8Weill Cornell Medical College, Obstetricsand Gynecology, Flushing, NY, 9Wayne State University, Obstetricsand Gynecology, Detroit, MI, 10Sequenom, Inc., Sequenom Centerfor Molecular Medicine, San Diego, CA, 11Sequenom, Inc. andSequenom Center for Molecular Medicine, Sequenom, Inc.and Sequenom Center for Molecular Medicine, San Diego, CAOBJECTIVE: To determine the accuracy of circulating cell-free fetalDNA (ffDNA) in each trimester of pregnancy in predicting fetal RhDstatus and fetal sex using a unique set of fetal identifiers.STUDY DESIGN: Patients underwent venipuncture in each trimester.Whole blood was centrifuged, separated into plasma and buffy coatand frozen at �80 degrees C. Samples were thawed and DNA analysiswas conducted via 4 allelle specific primers for the RHD gene and theRHD pseudogene and three Y-chromosome sequences (SRY, DBYand TTY2). In cases of an RHD negative, female result, reflex testing ofthe buffy coat and plasma DNAs to confirm the presence of ffDNAwas undertaken using a panel of 92 SNPs. A minimum of 6 informa-tive allelles, uniquely and unambiguously fetal in nature, establishedthe threshold. A cord blood sample was obtained at delivery and RhDtyping was utilized using standard serologic methods; phenotype as-sessment of the newborns was used to assign gender. Neonatal datawas entered into a web-based database. Laboratory personnel wereblinded to the neonatal data.RESULTS: 120 patients had their initial sample drawn at a median ges-tational age of 12.4 (range: 10.6-13.9) wks; at the second blood draw118 samples were drawn at 17.6 (16-20.9) wks; at the final blood draw113 samples were drawn at 28.7 (27.9-33.9) wks. Cord serology indi-cated 42 RhD positive females, 40 RhD positive males, 20 RhD nega-tive, females and 18 RhD, negative males. QNS or inconclusive sam-ples were noted in 12 (10%), 10 (8.5%) and 6 (5.3%) of cases in eachtrimester. Overall accuracy for RhD was 99.1%, 99.1% and 98.1% andwas 99.1%, 99.1% and 100% for fetal sex for each trimester, respec-tively (see table below).CONCLUSION: RHD typing and fetal sex can be very accurately deter-mined in all three trimesters using ffDNA in the maternal circulation.Reflex testing with a unique panel of SNPs allows for confirmation ofthe presence of fetal DNA. This assay is useful in the management ofRh sensitized pregnancies. The use of ffDNA to decide on candidatesfor antenatal Rhesus immune globulin warrants consideration.

709 Evaluation of the impact of maternal hyperglycemiaon fetal epigenetic inheritanceLaTasha Nelson1, Simon Lin2, Boyd Metzger3,Sharon Dooley1, William Lowe3

1Northwestern University Feinberg School of Medicine, Obstetrics andGynecology, Chicago, IL, 2Northwestern University Feinberg Schoolof Medicine, Clnical and Translational Sciences Institute, Chicago,IL, 3for the HAPO Study Cooperative Research Group,Northwestern University, Chicago, ILOBJECTIVE: To determine whether fetal epigenetic inheritance is asso-ciated with maternal hyperglycemia.STUDY DESIGN: A secondary analysis was performed utilizing samplesobtained during the Hyperglycemia and Adverse Pregnancy Outcome(HAPO) study. We selected a subset of participants from the Barbadosfield center who underwent an OGTT at 24-32 weeks gestation. Forthese analyses, 18 mother/baby pairs with a maternal fasting plasmaglucose (FPG) � 95 mg/dl were compared to 18 mother/baby pairswith a FPG level 2 and adjusted p-value � .05 used as the screeningcriteria. In addition, DNA methylation patterns in boy babies com-pared to girl babies were examined to assess for gender differences.Mothers were compared to female offspring to assess for differencesrelated to age.RESULTS: Methylation patterns were similar between mothers withhigh and low FPG; their neonates also demonstrated similar methyl-ation patterns. Evaluation for gender and age differences identified741 differential CpG sites between male and female infants (maxi-mum fold change of 43.8), as well as 1986 differential CpG sites be-tween mother and daughter samples (maximum fold change of 55.3).These differences persisted even after genes expressed on the sex chro-mosomes were excluded. The 741 sites which were determined toexhibit gender differences in our fetal subjects included 417 siteswhich previously have been identified as differentially expressed inadult subjects.CONCLUSION: Using Illumina HM27K microarray, no detectable pat-terns of methylation in maternal or neonatal white blood cells wererelated to the presence of maternal hyperglycemia. However, patternsof methylation were related to both gender and age.

710 A targeted approach for the prenatal detection ofcommon aneuploidies and 15 microdeletion syndromesLisa G. Shaffer1, J. Britt Ravnan1, Beth S. Torchia1, Jay W.Ellison1, Catherine D. Kashork1, Eric Deigan2, Pamela Herard2,Steven J. Thomas3, Samuel Bauer4, Jennifer Monroe5,Vinu D. Patel5, Sarah A. Reilly1, Justine Coppinger1

1Signature Genomic Laboratories, PerkinElmer Inc., Clinical Laboratory,Spokane, WA, 2Carolina Perinatal Associates, Ultrasound Center, Cary,NC, 3Center for Maternal Fetal Medicine, Perinatology, Las Vegas,NV, 4St. David’s Women’s Center of Texas, North Austin MaternalFetal Medicine, Austin, TX, 5Palm Beach Perinatal Center,Maternal Fetal Medicine, Boca Raton, FLOBJECTIVE: Tools are available to identify chromosome abnormalitiesin fetuses: karyotyping identifies large gains and losses, but the reso-lution limits the detection of abnormalities less than �10 Mb; FISHdetects aneuploidies or targeted microdeletion syndromes, but can-not interrogate entire genomes; and microarray testing examines en-tire genomes but may uncover alterations of unclear significance. Wereport our prospective findings using a novel assay that evaluates 15microdeletions and 5 common aneuploidies utilizing the Luminex

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