Application of risk score analysis to low‐coverage whole genome sequencing data for the noninvasive detection of trisomy 21, trisomy 18, and trisomy 13

American Journal of Obstetrics and Gynecology

Liu

et al. 2016

155

141

This study has demonstrated that genomewide NIPT for fetal chromosomal abnormalities can provide high resolution, sensitive, and specific detection of a wide range of subchromosomal and whole chromosomal abnormalities that were previously only detectable by invasive karyotype analysis. In some instances, this NIPT also provided additional clarification about the origin of genetic material that had not been identified by invasive karyotype analysis.

Section: Library Preparation Sequencing and Analytical Methodsmentioning

confidence: 99%

Clinical validation of a noninvasive prenatal test for genomewide detection of fetal copy number variants

Lefkowitz

American Journal of Obstetrics and Gynecology

Liu

et al. 2016

155

141

“…cfDNA was extracted from plasma using an automated extraction method with MyOne Dynabeads (Thermofisher Scientific, Waltham, MA). Plasma DNA was used to create indexed sequencing libraries as described by Tynan et al 14 Sequencing libraries were multiplexed, clustered, and sequenced on HiSeq 2000 or HiSeq 2500 instruments (Illumina, San Diego, CA), as described by Lefkowitz et al 13 Sequencing results were normalized and analyzed for fetal fraction; chromosome 21, 18, and 13 trisomy; sex chromosome aneuploidies; and other genome-wide whole-chromosome and subchromosome copy-number variants, using bioinformatics algorithms as previously described. 11,13,15 Data review Clinical laboratory directors reviewed sequencing data from each sample before the final reporting of results to the ordering clinician.…”

Section: Sample Laboratory Processingmentioning

confidence: 99%

Genome-wide cfDNA screening: clinical laboratory experience with the first 10,000 cases

Ehrich

Mazloom

et al. 2017

Genetics in Medicine

PurposeInvasive diagnostic prenatal testing can provide the most comprehensive information about the genetic status of a fetus. Noninvasive prenatal screening methods, especially when using cell-free DNA (cfDNA), are often limited to reporting only on trisomies 21, 18, and 13 and sex chromosome aneuploidies. This can leave a significant number of chromosomal and subchromosomal copy-number variations undetected. In 2015, we launched a new genome-wide cfDNA screening test that has the potential to narrow this detection gap.MethodsHere, we review the results from the first 10,000 cases submitted to the Sequenom clinical laboratory for genome-wide cfDNA screening.ResultsThe high-risk indication for this cohort differed compared with standard cfDNA screening. More samples were submitted with ultrasound indications (25% compared with 13% for standard cfDNA screening) and fewer for advanced maternal age (51% for genome-wide screening versus 68% for standard cfDNA screening). A total of 554 positive calls were made, of which 164 were detectable only via genome-wide analysis.ConclusionThis reports indicates a difference in utilization compared with standard cfDNA screening, where positivity rates are higher and a large subset of positive calls could not have been made using standard cfDNA screening.

“…Libraries were prepared and quantified as described by Tynan et al[13]. To reduce noise and increase signal, sequencing depth for this analysis was increased to target 32M reads per sample.…”

Section: Methodsmentioning

confidence: 99%

Clinical Validation of a Non-Invasive Prenatal Test for Genome-Wide Detection of Fetal Copy Number Variants

Lefkowitz

Liu

et al. 2015

Preprint

Abbreviations: bootstrap confidence level (BCL); chorionic villus sampling (CVS); 32 chromosomal abnormality decision tree (CADET); cell-free DNA (cfDNA); circular binary 33 segmentation (CBS); copy number variants (CNVs); non-invasive prenatal testing 34 (NIPT); sex chromosomal aneuploidies (SCAs); massively parallel sequencing (MPS), 35 triomsy 21 (T21); trisomy 18 (T18); trisomy 13 (T13) 36 ABSTRACT 38Background: Current cell-free DNA (cfDNA) assessment of fetal chromosomes does not 39 analyze and report on all chromosomes. Hence, a significant proportion of fetal chromosomal 40 abnormalities are not detectable by current non-invasive methods. Here we report the clinical 41 validation of a novel NIPT designed to detect genome-wide gains and losses of chromosomal 42 material ≥7 Mb and losses associated with specific deletions <7 Mb. 43Objective: The objective of this study is to provide a clinical validation of the sensitivity and 44 specificity of a novel NIPT for detection of genome-wide abnormalities. 45 Study Design: This retrospective, blinded study included maternal plasma collected from 1222 46 study subjects with pregnancies at increased risk for fetal chromosomal abnormalities that were 47 assessed for trisomy 21 (T21), trisomy 18 (T18), trisomy 13 (T13), sex chromosome 48 aneuploidies (SCAs), fetal sex, genome-wide copy number variants (CNVs) 7 Mb and larger, 49 and select deletions smaller than 7 Mb. Performance was assessed by comparing test results 50 with findings from G-band karyotyping, microarray data, or high coverage sequencing. 51Results: Clinical sensitivity within this study was determined to be 100% for T21, T18, T13, and 52 SCAs, and 97.7% for genome-wide CNVs. Clinical specificity within this study was determined 53 to be 100% for T21, T18, and T13, and 99.9% for SCAs and CNVs. Fetal sex classification had 54 an accuracy of 99.6%. 55 Conclusion:This study has demonstrated that genome-wide non-invasive prenatal testing 56 (NIPT) for fetal chromosomal abnormalities can provide high resolution, sensitive, and specific 57 detection of a wide range of sub-chromosomal and whole chromosomal abnormalities that were 58 previously only detectable by invasive karyotype analysis. In some instances, this NIPT also 59 provided additional clarification about the origin of genetic material that had not been identified 60 by invasive karyotype analysis. 61