Biology subjects

Kovacevic, V.

Publications and source records attributed to Kovacevic, V..

2 recordsLinked to original sources

bioRxiv2020

The first insight into the genetic structure of the population of modern Serbia

The complete understanding of the genomic contribution to complex traits, diseases, and response to treatments, as well as genomic medicine application to the well-being of all humans will be achieved through the global variome that encompasses fine-scale genetic diversity. Despite significant efforts in recent years, uneven representation still characterizes genomic resources and among the underrepresented European populations are the Western Balkans including the Serbian population. Our research addresses this gap and presents the first ever dataset of variants in clinically relevant genes in the population sample of contemporary Serbia. A few variants significantly more frequent in the analyzed sample population compared to the European population as a whole are distinguished as its unique genetic determinants. We explored thoroughly their potential functional impact and its correlation with the health burden of the population of Serbia. Our variants catalogue improves the understanding of genetics of modern Serbia, contributes to application of precision medicine and health equity. In addition, this resource may also be applicable in neighboring regions and in worldwide functional analyses of genetic variants in individuals of European descent.

genomics↗

bioRxiv2020

Benchmarking challenging small variants with linked and long reads

Genome in a Bottle (GIAB) benchmarks have been widely used to help validate clinical sequencing pipelines and develop new variant calling and sequencing methods. Here, we use accurate linked reads and long reads to expand the prior benchmarks in 7 samples to include difficult-to-map regions and segmental duplications that are not readily accessible to short reads. Our new benchmark adds more than 300,000 SNVs, 50,000 indels, and 16 % new exonic variants, many in challenging, clinically relevant genes not previously covered (e.g., PMS2). For HG002, we include 92% of the autosomal GRCh38 assembly, while excluding problematic regions for benchmarking small variants (e.g., copy number variants and reference errors) that should not have been in the previous version, which included 85% of GRCh38. By including difficult-to-map regions, this benchmark identifies eight times more false negatives in a short read variant call set relative to our previous benchmark.We have demonstrated the utility of this benchmark to reliably identify false positives and false negatives across technologies in more challenging regions, which enables continued technology and bioinformatics development.

genomics↗