March 24, 2022  |  

SFAF NGS Tech Panel (Teaser 2)

The COVID-19 pandemic has brought new focus and resources to pathogen surveillance of all kinds. HiFi sequencing, which combines high accuracy, long read lengths, and single-molecule sequencing, is unique in…

March 23, 2022  |  

Discoveries Roadshow

After two years apart, we’ve missed you, so we’re coming to a city near you. We are visiting 20 cities across North America and Europe during April and May. Join us…

December 20, 2021  |  

Long-read whole genome sequencing reveals HOXD13 alterations in synpolydactyly

Synpolydactyly 1 (SPD; MIM# 186000), also called syndactyly type II (SDTY2), is a genetic limb malformation characterized by polydactyly with syndactyly involving the webbing of the third and fourth fingers, and the fourth and fifth toes. It is caused by heterozygous alterations in HOXD13 with incomplete penetrance and phenotypic variability. In our study, a five-generation family with an SPD phenotype was enrolled in our Rare Disease Genomics Protocol. A comprehensive examination of three generations using Illumina short-read whole-genome sequencing (WGS) did not identify any causative variants. Subsequent WGS using Pacific Biosciences (PacBio) long-read HiFi Circular Consensus Sequencing (CCS) revealed a heterozygous 27-bp duplication in the polyalanine tract of HOXD13. Sanger sequencing of all available family members confirmed that the variant segregates with affected individuals. Re-analysis of an unrelated family with a similar SPD phenotype uncovered a 21-bp (7-alanine) duplication in the same region of HOXD13. Although ExpansionHunter identified these events in most individuals in a retrospective analysis, low sequence coverage due to high GC content in the HOXD13 polyalanine tract makes detection of these events challenging. Our findings highlight the value of long-read WGS in elucidating the molecular etiology of congenital limb malformation disorders.

November 16, 2021  |  

PacBio HiFiViral SARS-CoV-2 Kit

We created the HiFiViral SARS-CoV-2 Kit for labs working on the front line of the COVID-19 pandemic — tracking and identifying the spread of novel variants in their communities. The…

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