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Obstetrical & Gynecological Survey:
doi: 10.1097/01.ogx.0000429295.65513.69
Obstetrics: Genetics

Karyotype Versus Microarray Testing for Genetic Abnormalities After Stillbirth

Reddy, Uma M.; Page, Grier P.; Saade, George R.; Silver, Robert M.; Thorsten, Vanessa R.; Parker, Corette B.; Pinar, Halit; Willinger, Marian; Stoll, Barbara J.; Heim-Hall, Josefine; Varner, Michael W.; Goldenberg, Robert L.; Bukowski, Radek; Wapner, Ronald J.; Drews-Botsch, Carolyn D.; O’Brien, Barbara M.; Dudley, Donald J.; Levy, Brynn; for the NICHD Stillbirth Collaborative Research Network

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Abstract

Stillbirth occurs in 1 of every 160 births in the United States, but 25% to 60% remain unexplained. Karyotypic abnormalities are detected in 6% to 13% of stillbirths with a successful analysis. Microarray analysis can be performed on DNA from nonviable or macerated tissue. This study was designed to test the hypothesis that microarray analysis can detect abnormalities in stillbirth samples more often than karyotype analysis.

The Stillbirth Collaborative Research Network conducted a population-based study of stillbirth in a racially and ethnically diverse cohort in 5 geographic catchment areas. Standard postmortem examinations and karyotype analyses were performed. DNA from placenta and cord blood was stored for 2 to 5 years before microarray analysis. All copy-number variants of 500 kb or greater were included. Variants that were not identified in any of 3 databases were classified as probably benign, clinical significance unknown, or pathogenic. McNemar test for paired data was used to evaluate differences between karyotype and microarray analyses in the detection of variants.

Samples were obtained from 532 stillbirths from 524 pregnancies. Karyotyping of both fetal and placental tissue was done in 158 of 532 stillbirths (29.7%), fetal tissue only in 309 stillbirths (58.1%), placental tissue only in 64 stillbirths (12.0%), and tissue of unknown type in 1 stillbirth. Of the karyotype analyses, 375 (70.5%) yielded a result, of which 31 (8.3%) were classified as abnormal. Microarray analysis performed on the same 532 samples yielded a result in 465 stillbirths (87.4%), a significant difference from karyotyped samples (P < 0.001). In 396 (85.2%) of these 465 stillbirths, no variants greater than 500 kb, benign variants, or probably benign variants were observed. Microarray analysis provided improved detection of genomic abnormalities as compared with karyotype analysis (8.3% vs 5.8%, P = 0.007). When variants of unknown significance were included, microarray analysis provided even greater detection of abnormalities as compared with karyotyping (13.0% vs 5.8%, P < 0.001). Of the 157 stillbirths for which karyotype analysis failed to provide a definitive result, 79.6% yielded a definitive microarray result: 73.9% were normal or probably benign, and 5.7% were abnormal. Of the 31 stillbirths with abnormal karyotypes, 29 had results when submitted to microarray analysis. Karyotyping yielded a result in 298 (67.3%) of 443 antepartum stillbirths, of which 29 (9.7%) were abnormal, compared with a microarray result in 385 (86.9%) of these antepartum stillbirths, in which 31 (8.1%) were aneuploid, 8 (2.1%) had pathogenic variants, and 24 (6.2%) had variants of unknown significance. Microarray analysis detected more abnormalities in the antepartum subgroup than did karyotype analysis (8.8% vs 6.5%, P = 0.02), a 34.5% increase. Of the 472 stillbirths with postmortem examinations, 67 (14.2%) had structural anomalies. Karyotype analysis yielded results in 45 (67.2%) of these 67 stillbirths, of which 13 (28.9%) were abnormal. Microarray analysis was successful in 60 (89.6%) of the 67 stillbirths, of which 17 (28.3%) had aneuploidy, 3 (5.0%) had pathogenic variants, and 3 (5.0%) had variants of unknown significance.

The primary benefit of microarray over karyotype analysis is the greater likelihood of obtaining a result because of the ability to analyze nonviable tissue. Microarray analysis also is more sensitive to the presence of pathogenic variants and can identify more abnormalities of unknown significance. A major challenge with microarray testing in stillbirths is determining the clinical implications because the clinical relevance of many variants is unknown, which presents problems for genetic counseling. Microarray analysis is more expensive than standard karyotype analysis, but results in a higher yield of genomic abnormalities.

© 2013 by Lippincott Williams & Wilkins.

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