Browsing by Author "Behera, Sairam"

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    FixItFelix: improving genomic analysis by fixing reference errors
    (Springer Nature, 2023) Behera, Sairam; LeFaive, Jonathon; Orchard, Peter; Mahmoud, Medhat; Paulin, Luis F.; Farek, Jesse; Soto, Daniela C.; Parker, Stephen C. J.; Smith, Albert V.; Dennis, Megan Y.; Zook, Justin M.; Sedlazeck, Fritz J.
    The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including 12 with medical relevance. Here, we present FixItFelix, an efficient remapping approach, together with a modified version of the GRCh38 reference genome that improves the subsequent analysis across these genes within minutes for an existing alignment file while maintaining the same coordinates. We showcase these improvements over multi-ethnic control samples, demonstrating improvements for population variant calling as well as eQTL studies.
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    Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes
    (Springer Nature, 2023) Chin, Chen-Shan; Behera, Sairam; Khalak, Asif; Sedlazeck, Fritz J.; Sudmant, Peter H.; Wagner, Justin; Zook, Justin M.
    Advancements in sequencing technologies and assembly methods enable the regular production of high-quality genome assemblies characterizing complex regions. However, challenges remain in efficiently interpreting variation at various scales, from smaller tandem repeats to megabase rearrangements, across many human genomes. We present a PanGenome Research Tool Kit (PGR-TK) enabling analyses of complex pangenome structural and haplotype variation at multiple scales. We apply the graph decomposition methods in PGR-TK to the class II major histocompatibility complex demonstrating the importance of the human pangenome for analyzing complicated regions. Moreover, we investigate the Y-chromosome genes, DAZ1/DAZ2/DAZ3/DAZ4, of which structural variants have been linked to male infertility, and X-chromosome genes OPN1LW and OPN1MW linked to eye disorders. We further showcase PGR-TK across 395 complex repetitive medically important genes. This highlights the power of PGR-TK to resolve complex variation in regions of the genome that were previously too complex to analyze.
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    Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
    (Springer Nature, 2024) Kalef-Ezra, Ester; Turan, Zeliha Gozde; Perez-Rodriguez, Diego; Bomann, Ida; Behera, Sairam; Morley, Caoimhe; Scholz, Sonja W.; Jaunmuktane, Zane; Demeulemeester, Jonas; Sedlazeck, Fritz J.; Proukakis, Christos
    The presence of somatic mutations, including copy number variants (CNVs), in the brain is well recognized. Comprehensive study requires single-cell whole genome amplification, with several methods available, prior to sequencing. Here we compare PicoPLEX with two recent adaptations of multiple displacement amplification (MDA): primary template-directed amplification (PTA) and droplet MDA, across 93 human brain cortical nuclei. We demonstrate different properties for each, with PTA providing the broadest amplification, PicoPLEX the most even, and distinct chimeric profiles. Furthermore, we perform CNV calling on two brains with multiple system atrophy and one control brain using different reference genomes. We find that 20.6% of brain cells have at least one Mb-scale CNV, with some supported by bulk sequencing or single-cells from other brain regions. Our study highlights the importance of selecting whole genome amplification method and reference genome for CNV calling, while supporting the existence of somatic CNVs in healthy and diseased human brain.