Curated variation benchmarks for challenging medically-relevant autosomal genes
暂无分享,去创建一个
Mark T. W. Ebbert | Nathan D. Olson | Karen H. Miga | Wayne E. Clarke | Heng Li | J. Zook | S. Lincoln | C. Xiao | Justin Wagner | Arkarachai Fungtammasan | W. Rowell | J. Farek | F. Sedlazeck | Joyce Lee | A. Wenger | Haoyu Cheng | S. M. Sahraeian | G. Narzisi | J. M. Lorenzo-Salazar | Richa Gupta | David Jáspez | N. Olson | Alaina Shumate | Chen-Shan Chin | Yih-Chii Hwang | C. Flores | Lindsay Harris | U. S. Evani | L. A. Rubio-Rodríguez | Danny E. Miller | A. Muñoz-Barrera | M. Mahmoud | Christopher E. Mason | Jennifer McDaniel | M. Ebbert | B. Yoo | J. Lorenzo-Salazar | Ziad Khan | Aishwarya Pisupati | Yiming Zhu | Adrián Muñoz-Barrera | Carlos Flores | C. Mason | Chunlin Xiao | K. Miga
[1] Jordan M. Eizenga,et al. Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads , 2021, Nature Methods.
[2] Ryan M. Layer,et al. A complete reference genome improves analysis of human genetic variation , 2021, bioRxiv.
[3] Michael M. Khayat,et al. Exome variant discrepancies due to reference genome differences. , 2021, American journal of human genetics.
[4] F. Sedlazeck,et al. Towards population-scale long-read sequencing , 2021, Nature Reviews Genetics.
[5] Aaron M. Streets,et al. The complete sequence of a human genome , 2021, bioRxiv.
[6] Christopher A. Miller,et al. Failure to Detect Mutations in U2AF1 due to Changes in the GRCh38 Reference Sequence , 2021, bioRxiv.
[7] A. Sharp,et al. Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression. , 2021, American journal of human genetics.
[8] Jordan M. Eizenga,et al. Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks , 2021, bioRxiv.
[9] Heng Li,et al. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm , 2021, Nature Methods.
[10] Ryan L. Collins,et al. Author Correction: A structural variation reference for medical and population genetics , 2021, Nature.
[11] Steven L Salzberg,et al. Liftoff: accurate mapping of gene annotations , 2020, Bioinform..
[12] Kai Wang,et al. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions , 2020, bioRxiv.
[13] Heng Li,et al. The design and construction of reference pangenome graphs with minigraph , 2020, Genome biology.
[14] Yadong Wang,et al. Long-read-based human genomic structural variation detection with cuteSV , 2020, Genome Biology.
[15] Nathan D. Olson,et al. Benchmarking challenging small variants with linked and long reads , 2020, bioRxiv.
[16] S. Seal,et al. One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation , 2020, Genetics in Medicine.
[17] Ken Chen,et al. A robust benchmark for detection of germline large deletions and insertions , 2020, Nature Biotechnology.
[18] Ian T. Fiddes,et al. A robust benchmark for detection of germline large deletions and insertions , 2020, Nature Biotechnology.
[19] Sergey Koren,et al. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes , 2020, Nature Biotechnology.
[20] Tariq Ahmad,et al. A structural variation reference for medical and population genetics , 2020, Nature.
[21] Sergey Koren,et al. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads , 2020, bioRxiv.
[22] F. Mastaglia,et al. Structural Variants May Be a Source of Missing Heritability in sALS , 2020, Frontiers in Neuroscience.
[23] F. Sedlazeck,et al. Structural variant calling: the long and the short of it , 2019, Genome Biology.
[24] Alexander T. Dilthey,et al. A diploid assembly-based benchmark for variants in the major histocompatibility complex , 2019, Nature Communications.
[25] V. Bansal,et al. Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing , 2019, Nature Communications.
[26] Sergey Koren,et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome , 2019, Nature Biotechnology.
[27] Tanner D. Jensen,et al. Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight , 2019, Genome Biology.
[28] Birgit Funke,et al. Best practices for benchmarking germline small-variant calls in human genomes , 2019, Nature Biotechnology.
[29] W. Xiao,et al. Similarities and differences between variants called with human reference genome HG19 or HG38 , 2019, BMC Bioinformatics.
[30] Chunlin Xiao,et al. An open resource for accurately benchmarking small variant and reference calls , 2019, Nature Biotechnology.
[31] J. Casanova,et al. Rescue of recurrent deep intronic mutation underlying cell type–dependent quantitative NEMO deficiency , 2018, The Journal of clinical investigation.
[32] Thomas Colthurst,et al. A universal SNP and small-indel variant caller using deep neural networks , 2018, Nature Biotechnology.
[33] Hugo Y. K. Lam,et al. Deep convolutional neural networks for accurate somatic mutation detection , 2018, bioRxiv.
[34] Donna M. Muzny,et al. xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments , 2018, bioRxiv.
[35] Yeting Zhang,et al. Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects , 2018, Nature Communications.
[36] Wouter De Coster,et al. NanoPack: visualizing and processing long-read sequencing data , 2018, bioRxiv.
[37] T. Hayakawa,et al. Coevolution of Siglec-11 and Siglec-16 via gene conversion in primates , 2017, BMC Evolutionary Biology.
[38] Mauricio O. Carneiro,et al. Scaling accurate genetic variant discovery to tens of thousands of samples , 2017, bioRxiv.
[39] Heng Li,et al. Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..
[40] Michael C. Schatz,et al. Accurate detection of complex structural variations using single molecule sequencing , 2017, Nature Methods.
[41] Yan Guo,et al. Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis. , 2017, Genomics.
[42] Daniel L. Cameron,et al. GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly , 2017, bioRxiv.
[43] Shilpa Garg,et al. WhatsHap: fast and accurate read-based phasing , 2016, bioRxiv.
[44] F. Balloux,et al. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast , 2016, Nature Communications.
[45] Birgit Funke,et al. Navigating highly homologous genes in a molecular diagnostic setting: a resource for clinical next-generation sequencing , 2016, Genetics in Medicine.
[46] Xiaoyu Chen,et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications , 2016, Bioinform..
[47] F. Kronenberg,et al. Structure, function, and genetics of lipoprotein (a) , 2016, Journal of Lipid Research.
[48] Rachel L. Goldfeder,et al. Medical implications of technical accuracy in genome sequencing , 2016, Genome Medicine.
[49] Mark Yandell,et al. Wham: Identifying Structural Variants of Biological Consequence , 2015, PLoS Comput. Biol..
[50] Gabor T. Marth,et al. A global reference for human genetic variation , 2015, Nature.
[51] Alexa B. R. McIntyre,et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials , 2015, Scientific Data.
[52] Leo van Iersel,et al. WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads , 2015, J. Comput. Biol..
[53] Edwin Cuppen,et al. Sambamba: fast processing of NGS alignment formats , 2015, Bioinform..
[54] Christina A. Cuomo,et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.
[55] Ira M. Hall,et al. SAMBLASTER: fast duplicate marking and structural variant read extraction , 2014, Bioinform..
[56] N. Lennon,et al. Characterizing and measuring bias in sequence data , 2013, Genome Biology.
[57] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[58] Ryan M. Layer,et al. LUMPY: a probabilistic framework for structural variant discovery , 2012, Genome Biology.
[59] V. Beneš,et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis , 2012, Bioinform..
[60] Euan A Ashley,et al. A public resource facilitating clinical use of genomes , 2012, Proceedings of the National Academy of Sciences.
[61] C. Cole,et al. COSMIC: the catalogue of somatic mutations in cancer , 2011, Genome Biology.
[62] A. Feinberg,et al. Addition of H19 'loss of methylation testing' for Beckwith-Wiedemann syndrome (BWS) increases the diagnostic yield. , 2010, The Journal of molecular diagnostics : JMD.
[63] A. Towbin,et al. Chronic granulomatous disease , 2010, Pediatric Radiology.
[64] Aaron R. Quinlan,et al. BIOINFORMATICS APPLICATIONS NOTE , 2022 .
[65] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[66] H. Innan. A two-locus gene conversion model with selection and its application to the human RHCE and RHD genes , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[67] I. Biros,et al. Spinal muscular atrophy: untangling the knot? , 1999, Journal of medical genetics.
[68] J. Melki,et al. Spinal muscular atrophy. , 1997, Current opinion in neurology.