Human Genome Mapping Gaps Found by Latest Technology

Thousands of never-before-seen genetic variants in the human genome have been uncovered using a new genome sequencing technology and these discoveries close many human genome mapping gaps that have long resisted sequencing.

The human genome is arguably the most complete mammalian reference assembly, yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. Euchromatin is chromosomal material that is genetically active and stains lightly with basic dyes.

A team of scientists led by those at University of Washington School of Medicine (Seattle, WA, USA) identified missing sequence and genetic variation, by sequencing and analyzing a haploid human genome Leukocyte Cell Derived Chemotaxin 1 (CHM1) using single-molecule, real-time DNA sequencing.

The technique used is called single-molecule, real-time DNA sequencing (SMRT), which may now make it possible for investigators to identify potential genetic mutations behind many conditions whose genetic causes have long eluded scientists. SMRT whole genome sequencing (WGS) data with 41-fold sequence coverage was generated using a PacBio RSII instrument (Pacific Biosciences Menlo Park, CA, USA) from genomic libraries generated from a complete hydatidiform mole DNA (CHM1tert).

This approach successfully pinpointed millions of small variations in the human genome. These variations arise from substitution of a single nucleotide base, called a single-nucleotide polymorphisms or SNP. The standard approach also made it possible to identify very large variations, typically involving segments of DNA that are 5,000 bases long or longer. But for technical reasons, scientists had previously not been able to reliably detect variations whose lengths are in between, those ranging from about 50 to 5,000 bases in length. The SMRT technology used in the study made it possible to sequence and read DNA segments longer than 5,000 bases, far longer than standard gene sequencing technology. The team was able to identify and sequence 26,079 segments that were different from a standard human reference genome used in genome studies and most of these variants, about 22,000, have never been reported before.

Evan E. Eichler, professor of genome sciences and senior author of the study said, “In five years there might be a long-read sequence technology that will allow clinical laboratories to sequence a patient's chromosomes from tip to tip and say, 'Yes, you have about three to four million SNPs and insertions deletions but you also have approximately 30,000–40,000 structural variants. Of these, a few structural variants and a few SNPs are the reason why you're susceptible to this disease.' Knowing all the variation is going to be a game changer.” The study was published on November 10, 2014, in the journal Nature.

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University of Washington School of Medicine 
Pacific Biosciences