Scientists at Stanford University and the Icahn School of Medicine at Mount Sinai have made impressive strides in resolving variants in the SLC6A4 promoter associated with susceptibility to psychiatric disorders and response to antidepressants. This progress was made possible with highly accurate, long-read sequencing, known as HiFi sequencing. Published in the journal Genes, the paper comes from lead author Mariana Botton, senior author Stuart Scott, and collaborators. It describes a SMRT Sequencing-based approach to analyzing amplicons of the SLC6A4 promoter region, which is noted for “a variable number of homologous 20–24 bp repeats,” the authors write, as well as long, extra-long,…
The ploidy or number of copies of each chromosome in a genome affects not only the size but also the complexity of the genome. Geneticists often point out that a human does not have “a” genome but rather two genomes, one inherited from the mother and another from the father. The number of complete sets of chromosomes in each cell, or haplotypes, is referred to as ploidy. Humans and most other animals are diploid (2N), having two sets. Many plants have higher ploidy, for example, the hexaploid (6N) California Redwood has 6 copies of each chromosome. The number of chromosome…
On the heels of her remarkable paper tracing influenza evolution in a single host last spring, New York University’s Elodie Ghedin has come out with a new publication in Nature Genetics that offers a higher-resolution view of how the flu spreads through a population. From lead author Leo Poon at the University of Hong Kong and senior author Ghedin, “Quantifying influenza virus diversity and transmission in humans” reports the results of an international collaboration to track the Hong Kong flu pandemic of 2009. The authors began with the premise that much about the genetically diverse influenza A virus is unknown,…
Mendelspod host Theral Timpson recently interviewed Professor Steven Marsh, Director of Bioinformatics at the Anthony Nolan Research Institute, a UK-based organization dedicated to improving the outcomes of bone marrow transplantation and host to the world’s first bone marrow registry. Prof. Marsh and his team have dramatically improved the resolution of HLA typing — one of the methods used for matching compatible donors with transplant recipients — using long, accurate reads from PacBio sequencing. Their fascinating conversation covers the past, present, and future of HLA typing — highlights are below. Short History of HLA Typing — There’s a Lot More Diversity…