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Evaluation of Liftover Tools for the Conversion of Genome Reference Consortium Human Build 37 to Build 38 Using ClinVar Variants

Although Genome Reference Consortium Human Build 38 (GRCh38) was released with improvement over GRCh37, it has not been widely adopted. Several liftover tools have been developed as a convenient approach for GRCh38 implementation. This study aimed to investigate the accuracy of liftover tools for ge...

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Autores principales: Park, Kyoung-Jin, Yoon, Young Ahn, Park, Jong-Ho
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10606611/
https://www.ncbi.nlm.nih.gov/pubmed/37895222
http://dx.doi.org/10.3390/genes14101875
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author Park, Kyoung-Jin
Yoon, Young Ahn
Park, Jong-Ho
author_facet Park, Kyoung-Jin
Yoon, Young Ahn
Park, Jong-Ho
author_sort Park, Kyoung-Jin
collection PubMed
description Although Genome Reference Consortium Human Build 38 (GRCh38) was released with improvement over GRCh37, it has not been widely adopted. Several liftover tools have been developed as a convenient approach for GRCh38 implementation. This study aimed to investigate the accuracy of liftover tools for genome conversion. Two Variant Call Format (VCF) files aligned to GRCh37 and GRCh38 were downloaded from ClinVar (clinvar_20221217.vcf.gz). Liftover tools such as CrossMap, NCBI Remap, and UCSC liftOver were used to convert genome coordinates from GRCh37 to GRCh38. The accuracy of CrossMap, NCBI Remap, and UCSC liftOver were 99.81% (1,567,838/1,570,748), 99.69% (1,565,953/1,570,748), and 99.99% (1,570,550/1,570,748), respectively. Variants that failed conversion via all three liftover tools were all indels/duplications: a pathogenic/likely pathogenic variant (n = 1) and benign/likely benign variants (n = 7). The eight variants that failed conversion were identified in the ALMS, TTN, CFTR, SLCO, LDLR, PCNT, MID1, and GRIA3 genes, and all the variants were not in the VCF files aligned to GRCh37. This study demonstrated that three liftover tools could successfully convert reference genomes from GRCh37 to GRCh38 in more than 99% of ClinVar variants. This study takes the first step to clinically implement GRCh38 using liftover tools. Further clinical studies are warranted to compare the performance of liftover tools and to validate re-alignment approaches in routine clinical settings.
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spelling pubmed-106066112023-10-28 Evaluation of Liftover Tools for the Conversion of Genome Reference Consortium Human Build 37 to Build 38 Using ClinVar Variants Park, Kyoung-Jin Yoon, Young Ahn Park, Jong-Ho Genes (Basel) Article Although Genome Reference Consortium Human Build 38 (GRCh38) was released with improvement over GRCh37, it has not been widely adopted. Several liftover tools have been developed as a convenient approach for GRCh38 implementation. This study aimed to investigate the accuracy of liftover tools for genome conversion. Two Variant Call Format (VCF) files aligned to GRCh37 and GRCh38 were downloaded from ClinVar (clinvar_20221217.vcf.gz). Liftover tools such as CrossMap, NCBI Remap, and UCSC liftOver were used to convert genome coordinates from GRCh37 to GRCh38. The accuracy of CrossMap, NCBI Remap, and UCSC liftOver were 99.81% (1,567,838/1,570,748), 99.69% (1,565,953/1,570,748), and 99.99% (1,570,550/1,570,748), respectively. Variants that failed conversion via all three liftover tools were all indels/duplications: a pathogenic/likely pathogenic variant (n = 1) and benign/likely benign variants (n = 7). The eight variants that failed conversion were identified in the ALMS, TTN, CFTR, SLCO, LDLR, PCNT, MID1, and GRIA3 genes, and all the variants were not in the VCF files aligned to GRCh37. This study demonstrated that three liftover tools could successfully convert reference genomes from GRCh37 to GRCh38 in more than 99% of ClinVar variants. This study takes the first step to clinically implement GRCh38 using liftover tools. Further clinical studies are warranted to compare the performance of liftover tools and to validate re-alignment approaches in routine clinical settings. MDPI 2023-09-26 /pmc/articles/PMC10606611/ /pubmed/37895222 http://dx.doi.org/10.3390/genes14101875 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Park, Kyoung-Jin
Yoon, Young Ahn
Park, Jong-Ho
Evaluation of Liftover Tools for the Conversion of Genome Reference Consortium Human Build 37 to Build 38 Using ClinVar Variants
title Evaluation of Liftover Tools for the Conversion of Genome Reference Consortium Human Build 37 to Build 38 Using ClinVar Variants
title_full Evaluation of Liftover Tools for the Conversion of Genome Reference Consortium Human Build 37 to Build 38 Using ClinVar Variants
title_fullStr Evaluation of Liftover Tools for the Conversion of Genome Reference Consortium Human Build 37 to Build 38 Using ClinVar Variants
title_full_unstemmed Evaluation of Liftover Tools for the Conversion of Genome Reference Consortium Human Build 37 to Build 38 Using ClinVar Variants
title_short Evaluation of Liftover Tools for the Conversion of Genome Reference Consortium Human Build 37 to Build 38 Using ClinVar Variants
title_sort evaluation of liftover tools for the conversion of genome reference consortium human build 37 to build 38 using clinvar variants
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10606611/
https://www.ncbi.nlm.nih.gov/pubmed/37895222
http://dx.doi.org/10.3390/genes14101875
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