Bioinformaticians compute gene sequences inherited from each parent

Humans have 46 chromosomes. To ensure that the number of chromosomes does not double with each generation, only 23 chromosomes are included in male and female germ cells, which merge in a fertilized egg cell to form an embryo. Such a half-set of chromosomes is designated as "haploid."

"Which gene variants I receive from my father or mother can decide whether I get sick, and also how I can best be medically treated," explains Tobias Marschall, Professor of Bioinformatics at Saarland University.

Being able to analyze which gene variants were inherited from which parent, and thereby determine the so-called haplotype, is a quantum leap for the sequencing of the human genome. Two developments are crucial for this: First, the so-called third-generation sequencing techniques, established by firms like Oxford Nanopore, 10x Genomics and Pacific Biosciences, deliver a different type of gene data. "We now get much longer gene snippets, and can finally put into practice what we have long studied in theory," says Marschall. He is actively involved in the second effort: He develops the computational methods that make the mountains of genetic data manageable. He has developed a software package called WhatsHap with his colleagues.

"Imagine an extremely difficult puzzle. With WhatsHap, we solve two of them at the same time," Marschall says. He is convinced that with the help of such programs, in the foreseeable future the determination of one's haplotype will become a routine examination in hospitals, just as identification of the blood group is today. He considers the two articles in the journal Nature Communications the first milestone for this.

More information:
David Porubsky et al, Dense and accurate whole-chromosome haplotyping of individual genomes, Nature Communications (2017). DOI: 10.1038/s41467-017-01389-4

Provided by Saarland University