This STAT test is for prenatal use and involves sequencing the whole exome with a mean coverage of 100x, enhanced coverage of known disease-causing genes, and curated deep-intronic variants. The WES test will reliably detect the majority of copy number variations (CNVs) of 3 exons or greater. Smaller CNV events may also be detected and reported, but additional follow-up testing is recommended if a smaller CNV is suspected. The WES assay will also detect microdeletion/duplication events greater than 500kb in clinically relevant regions, although follow-up testing may be warranted to better delineate the exact size of the event and confirm breakpoints. Secondary findings per American College of Medical Genetics (ACMG) recommendations may be requested; however, secondary findings will not be reported for ongoing pregnancies. Proband only, duo, trio and quad testing options are available, with parental reports included on duo, trio and quad testing if specifically requested.

Maternal cell contamination (MCC) is offered as a stand-alone test and is required to accompany prenatal testing for samples derived from amniotic fluid, and chorionic villi sampling. MCC study can be requested on other prenatal / fetal samples at the ordering provider's discretion.

• Increased NT/cystic hygroma
• Fetal anomaly

The purpose of this test is to find the underlying genetic cause for the prenatal findings.

Sequencing is performed on genomic DNA enriched for the exome using a sequence capture method. Direct sequencing of the amplified captured regions was performed using 2X150bp reads on Illumina next-generation sequencing (NGS) systems. A base has sufficient coverage at 20X, and an exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered at 20X or more. If any, a list of low-coverage regions is available upon request. Alignment to the human reference genome (hg19) is performed, and annotated variants are identified in the targeted region. Variants reviewed have a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Indels and single nucleotide variants (SNVs) may be confirmed by Sanger sequence analysis before reporting at the director's discretion. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter, and enhancer regions, and areas containing large numbers of tandem repeats. This assay does not cover genes and exons located in pseudogene regions. Copy number variation (CNV) analysis detects deletions and duplications; in some instances, due to the size of the exons, sequence complexity, or other factors, not all CNVs may be analyzed or may be difficult to detect. CNV analysis will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), methylation abnormalities, triploidy, and genomic imbalances in segmentally duplicated regions. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Primary data analysis is performed using Illumina bcl2fastq converter v2.19. Secondary analysis is performed using Illumina DRAGEN Bio-IT Platform v.3.4.12. Tertiary data analysis is performed using SnpEff v4.3t and Revvity Omics' internal ODIN v.1.01 software. CNV and absence of heterozygosity are assessed using BioDiscovery’s NxClinical v6.1 software.