Genome Sequencing Increases Sensitivity of Carrier Screens

More recently, lower sequencing costs coupled with higher accuracy of next generation sequencing-based methodologies have made it affordable for clinical laboratories to offer screening for substantially more conditions.

Massively parallel sequencing or next-generation sequencing (NGS) has provided the technical means to not only screen the full gene, but also analyze multiple genes and multiple individuals simultaneously, as compared to the targeted mutation panel approach of traditional carrier screening. However, given the rapid pace of its application, there is a paucity of information on the downstream impact of NGS in the healthcare system and in routine medical care.

A large team of scientists collaborating with their colleagues at the Oregon Health & Science University (Portland, OR, USA) first sequenced the genomes of 131 women, all members of the Kaiser Permanente Northwest healthcare system. For those with a positive carrier result, the scientists invited their male partners to get tested, resulting in 71 additional genomes sequenced. The team analyzed the data for variants in 728 genes related to inherited disease, including autosomal-recessive and X-linked conditions. They included lifespan-limiting, serious, mild, unpredictable, and adult-onset disorders. In addition, they looked for medically actionable variants, so-called secondary findings, in 148 genes, which included the American College of Medical Genetics and Genomics' 59-gene list.

The investigators extracted DNA from the participant’s blood and processed for sequencing using the Illumina TruSeq DNA LT kit. The DNA sample was sequenced on a HiSeq 2000 or 2500 (Illumina, version 3 chemistry) with 100 base pair, paired-end reads. The sequenced fragments were assessed for quality and aligned to the NCBI reference genome (GRCh37/hg19) to generate BAM files. Single-Nucleotide Variants (SNV) and Small Insertion and Deletions (Indel) were assigned. Structural variant analysis of the sequencing data were defined that included 2,000 nucleotides upstream and downstream of the first and last exon in the longest transcript. Tertiary Analysis and Variant Confirmation for SNVs and CNVs were also performed.

The scientists reported the results were in two phases: first the carrier results and later the medically actionable secondary findings. All participants received results for the lifespan-limiting conditions of the carrier screen, whereas the other results were optional. Of note, 93% of participants opted to receive all categories of carrier results, and 99% asked for their medically actionable secondary findings. Of the 202 participants, 78% received at least one positive carrier result, and the number of variants reported per person range from zero to five.

Twelve of the 71 couples tested turned out to be carriers for the same condition, and three women were carriers for an X-linked condition. Seven individuals, or 3.5% of participants, received secondary findings, and all but one of these would have been picked up by the American College of Medical Genetics and Genomics (ACMG)-59 list. The analysis also resulted in 808 variants of unknown significance, an average of four per person, which were not reported.

The authors concluded that overall, next-gen-sequencing-based carrier screening panels can detect rarer and novel pathogenic variants than traditional mutation screening panels that are designed for specific ethnic groups, and whole-genome sequencing can get around some of the biases and errors associated with targeted sequencing, and provide better structural variant detection. The study was published on May 10, 2018, in the journal American Journal of Human Genetics.

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Oregon Health & Science University