FixItFelix: improving genomic analysis by fixing reference errors

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 e...

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Vydané v:	Genome Biology Ročník 24; číslo 1; s. 31
Hlavní autori:	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.
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	London BioMed Central 21.02.2023 Springer Nature B.V BMC
Predmet:	Animal Genetics and Genomics Bioinformatics Biomedical and Life Sciences Evolutionary Biology genome Genome, Human Genomes Genomic analysis Genomics GRCh38 High-Throughput Nucleotide Sequencing Human Genetics Humans INDEL Life Sciences Method Microbial Genetics and Genomics nationalities and ethnic groups Plant Genetics and Genomics Sequence Analysis, DNA SNV T2T-CHM13 Variant Variant GIAB T2T-CHM13 Remapping Reference SNV eQTL Medically relevant genes GRCh38 INDEL
ISSN:	1474-760X, 1474-7596, 1474-760X
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Abstract	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.
AbstractList	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. 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.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. Abstract 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.
ArticleNumber	31
Author	Orchard, Peter Sedlazeck, Fritz J. Mahmoud, Medhat LeFaive, Jonathon Dennis, Megan Y. Farek, Jesse Soto, Daniela C. Behera, Sairam Paulin, Luis F. Parker, Stephen C. J. Smith, Albert V. Zook, Justin M.
Author_xml	– sequence: 1 givenname: Sairam surname: Behera fullname: Behera, Sairam organization: Human Genome Sequencing Center, Baylor College of Medicine – sequence: 2 givenname: Jonathon surname: LeFaive fullname: LeFaive, Jonathon organization: Department of Biostatistics, University of Michigan School of Public Health – sequence: 3 givenname: Peter surname: Orchard fullname: Orchard, Peter organization: Department of Computational Medicine and Bioinformatics, University of Michigan – sequence: 4 givenname: Medhat surname: Mahmoud fullname: Mahmoud, Medhat organization: Human Genome Sequencing Center, Baylor College of Medicine – sequence: 5 givenname: Luis F. surname: Paulin fullname: Paulin, Luis F. organization: Human Genome Sequencing Center, Baylor College of Medicine – sequence: 6 givenname: Jesse surname: Farek fullname: Farek, Jesse organization: Human Genome Sequencing Center, Baylor College of Medicine – sequence: 7 givenname: Daniela C. surname: Soto fullname: Soto, Daniela C. organization: Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis – sequence: 8 givenname: Stephen C. J. surname: Parker fullname: Parker, Stephen C. J. organization: Department of Computational Medicine and Bioinformatics, University of Michigan – sequence: 9 givenname: Albert V. surname: Smith fullname: Smith, Albert V. organization: Department of Biostatistics, University of Michigan School of Public Health – sequence: 10 givenname: Megan Y. surname: Dennis fullname: Dennis, Megan Y. organization: Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis – sequence: 11 givenname: Justin M. surname: Zook fullname: Zook, Justin M. email: justin.zook@nist.gov organization: Material Measurement Laboratory, National Institute of Standards and Technology – sequence: 12 givenname: Fritz J. orcidid: 0000-0001-6040-2691 surname: Sedlazeck fullname: Sedlazeck, Fritz J. email: Fritz.Sedlazeck@bcm.edu organization: Human Genome Sequencing Center, Baylor College of Medicine, Department of Computer Science, Rice University
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/36810122$$D View this record in MEDLINE/PubMed
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Snippet	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... Abstract 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...
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SubjectTerms	Animal Genetics and Genomics Bioinformatics Biomedical and Life Sciences Evolutionary Biology genome Genome, Human Genomes Genomic analysis Genomics GRCh38 High-Throughput Nucleotide Sequencing Human Genetics Humans INDEL Life Sciences Method Microbial Genetics and Genomics nationalities and ethnic groups Plant Genetics and Genomics Sequence Analysis, DNA SNV T2T-CHM13 Variant
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Title	FixItFelix: improving genomic analysis by fixing reference errors
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