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Curated variation benchmarks for challenging medically relevant autosomal genes
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Abstract
The repetitive nature and complexity of some medically relevant genes poses a challenge for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has provided variant benchmark sets, but these exclude nearly 400 medically relevant genes due to their repetitiveness or polymorphic complexity. Here, we characterize 273 of these 395 challenging autosomal genes using a haplotype-resolved whole-genome assembly. This curated benchmark reports over 17,000 single-nucleotide variations, 3,600 insertions and deletions and 200 structural variations each for human genome reference GRCh37 and GRCh38 across HG002. We show that false duplications in either GRCh37 or GRCh38 result in reference-specific, missed variants for short- and long-read technologies in medically relevant genes, including CBS, CRYAA and KCNE1. When masking these false duplications, variant recall can improve from 8% to 100%. Forming benchmarks from a haplotype-resolved whole-genome assembly may become a prototype for future benchmarks covering the whole genome.
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The GIAB CMRG benchmark spans 273 medically relevant genes that are highly repetitive and diverse and were excluded from the genome-wide benchmark.
“This GIAB benchmark spans 273 medically relevant genes that are highly repetitive and diverse and were therefore excluded from the genome-wide benchmark12.”
From Comprehensive genome analysis and variant detection at scale using DRAGEN (2025) · cites this paper as [12]
The Introduction says the CMRG benchmark covers 273 medically relevant genes that were incompletely covered by previous GIAB benchmarks, and the Results describe these genes as substantially more challenging. But the Introduction specifies that up to 90% of each gene’s bases were already included, so saying the genes were excluded from the genome-wide benchmark overstates the finding. The paper describes several kinds of challenges, not every gene as both highly repetitive and diverse. (LLM, conf=0.86)
Experimental — accuracy not yet measuredFor SNVs, benchmarking was performed on both genome-wide (NIST GIAB v.4.2.1 high-confidence regions) and CMRG regions (GIAB v.1.0).
“For SNVs, benchmarking was performed on both genome-wide (NIST GIAB v.4.2.1 high-confidence regions) and CMRG regions (GIAB v.1.0) (ref. 12).”
From Comprehensive genome analysis and variant detection at scale using DRAGEN (2025) · cites this paper as [12]
PanGenie genotyping of HG002 based on SVs at challenging medically relevant loci resulted in a precision of 0.74 and an adjusted recall of 0.81.
“Furthermore, we used PanGenie to genotype HG002 and evaluated genotypes based on SVs at challenging medically relevant loci47. This analysis resulted in a precision of 0.74 and an adjusted recall of 0.81 (Methods).”
From A draft human pangenome reference. (2023) · cites this paper as [47]
These benefits were greatest at complex loci.
“These benefits were also greatest at complex loci47.”
From A draft human pangenome reference. (2023) · cites this paper as [47]
The CHM13-based pangenome offers the largest gains in variant calling in challenging regions like those assessed by the CMRG truth set.
“Unsurprisingly, the CHM13-based pangenome offers the largest gains in variant calling in challenging regions like those assessed by the Challenging Medically Relevant Genes (CMRG) truth set (Fig. 2e) 29 .”
From Pangenome graph construction from genome alignments with Minigraph-Cactus (2024) · cites this paper as [29]
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Self-citationBEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247
Self-citationMinimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807
Self-citationWalker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J. R., Young, S., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0112963 · Cited by 9,130
MIMIC-III, a freely accessible critical care database
Johnson, A. E. W., Pollard, T. J., Shen, L., Lehman, L.-W. H., Feng, M., Ghassemi, M., Moody, B., Szolovits, P., Anthony Celi, L., & Mark, R. G. (2016) · Scientific Data · doi:10.1038/sdata.2016.35 · Cited by 8,141
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., & Li, H. (2021) · Nature Methods · doi:10.1038/s41592-020-01056-5 · Cited by 5,859
Self-citationCOSMIC: the Catalogue Of Somatic Mutations In Cancer
Tate, J. G., Bamford, S., Jubb, H. C., Sondka, Z., Beare, D. M., Bindal, N., Boutselakis, H., Cole, C. G., Creatore, C., Dawson, E., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1015 · Cited by 4,867
Performance of neural network basecalling tools for Oxford Nanopore sequencing
Wick, R. R., Judd, L. M., & Holt, K. E. (2019) · Genome Biology · doi:10.1186/s13059-019-1727-y · Cited by 3,221
NanoPack: visualizing and processing long-read sequencing data
De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty149 · Cited by 3,168
Opportunities and challenges in long-read sequencing data analysis
Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020) · Genome Biology · doi:10.1186/s13059-020-1935-5 · Cited by 2,530
DELLY: structural variant discovery by integrated paired-end and split-read analysis
Rausch, T., Zichner, T., Schlattl, A., Stütz, A. M., Beneš, V., & Korbel, J. O. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts378 · Cited by 2,438
SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells
Sachs, P., Ding, D., Bergmaier, P., Lamp, B., Schlagheck, C., Finkernagel, F., Nist, A., Stiewe, T., & Mermoud, J. E. (2019) · Nature Communications · doi:10.1038/s41467-019-09078-0 · Cited by 2,400
Sambamba: fast processing of NGS alignment formats
Tarasov, A., Vilella, A. J., Cuppen, E. P. J. G., Nijman, I. J., & Prins, P. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv098 · Cited by 2,384
Scaling accurate genetic variant discovery to tens of thousands of samplesPreprint
Poplin, R. E., Ruano-Rubio, V., DePristo, M. A., Fennell, T. J., Carneiro, M. O., der Auwera, G. A. V., Kling, D. E., Gauthier, L. D., Levy‐Moonshine, A., Roazen, D., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/201178 · Cited by 1,977
Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0217-9 · Cited by 1,841
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Poplin, R., Chang, P.-C., Alexander, D., Schwartz, S., Colthurst, T., Ku, A., Newburger, D., Dijamco, J., Nguyen, N., Afshar, P. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4235 · Cited by 1,840
Accurate detection of complex structural variations using single-molecule sequencing
Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., & Schatz, M. C. (2018) · Nature Methods · doi:10.1038/s41592-018-0001-7 · Cited by 1,601
Self-citationLUMPY: a probabilistic framework for structural variant discovery
Layer, R. M., Chiang, C., Quinlan, A. R., & Hall, I. M. (2014) · Genome biology · doi:10.1186/gb-2014-15-6-r84 · Cited by 1,544
A structural variation reference for medical and population genetics
Collins, R. L., Brand, H., Karczewski, K. J., Zhao, X., Alföldi, J., Francioli, L. C., Khera, A. V., Lowther, C., Gauthier, L. D., Wang, H., et al. (2020) · Nature · doi:10.1038/s41586-020-2287-8 · Cited by 1,037
Liftoff: accurate mapping of gene annotations
Shumate, A., & Salzberg, S. L. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa1016 · Cited by 991
Self-citationCharacterizing and measuring bias in sequence data
Ross, M. G., Russ, C., Costello, M., Hollinger, A., Lennon, N. J., Hegarty, R., Nusbaum, C., & Jaffe, D. B. (2013) · Genome Biology · doi:10.1186/gb-2013-14-5-r51 · Cited by 909
SAMBLASTER : fast duplicate marking and structural variant read extraction
Faust, G. G., & Hall, I. M. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu314 · Cited by 880
Extensive sequencing of seven human genomes to characterize benchmark reference materials
Zook, J. M., Catoe, D., McDaniel, J., Vang, L., Spies, N., Sidow, A., Weng, Z., Liu, Y., Mason, C. E., Alexander, N., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.25 · Cited by 811
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“1 are still excluded from the CMRG benchmark (110 on GRCh37 and 100 on GRCh38) for multiple reasons detailed in Supplementary Data 7: When progressively categorizing excluded genes on GRCh38, (1) 20 genes were affected by gaps in the reference, (2) 38 genes had evidence of duplications in HG002 relative to GRCh38, (3)…”
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Shafin, K., Pesout, T., Lorig-Roach, R., Haukness, M., Olsen, H. E., Bosworth, C., Armstrong, J., Tigyi, K., Maurer, N., Koren, S., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0503-6 · Cited by 567
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Li, H., Feng, X., & Chu, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02168-z · Cited by 455
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Patterson, M., Marschall, T., Pisanti, N., van Iersel, L., Stougie, L., Klau, G. W., & Schönhuth, A. (2015) · Journal of Computational Biology · doi:10.1089/cmb.2014.0157 · Cited by 453
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Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., et al. (2022) · Science · doi:10.1126/science.abl3533 · Cited by 441
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Self-citationCameron, D., Schröder, J., Penington, J. S., Do, H., Molania, R., Dobrovic, A., Speed, T. P., & Papenfuss, A. T. (2017) · Genome Research · doi:10.1101/gr.222109.117 · Cited by 377
Greninger, A. L., Messacar, K., Dunnebacke, T. H., Naccache, S. N., Federman, S., Bouquet, J., Mirsky, D. M., Nomura, Y., Yagi, S., Glaser, C. A., et al. (2016) · Genome Medicine · doi:10.1186/s13073-015-0257-9 · Cited by 333
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De Coster, W., Weissensteiner, M. H., & Sedlazeck, F. J. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00367-3 · Cited by 323
Self-citationShafin, K., Pesout, T., Chang, P.-C., Nattestad, M., Kolesnikov, A., Goel, S., Baid, G., Kolmogorov, M., Eizenga, J. M., Miga, K. H., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01299-w · Cited by 311
Self-citationEdge, P., & Bansal, V. (2019) · Nature Communications · doi:10.1038/s41467-019-12493-y · Cited by 252
Mandelker, D. L., Schmidt, R. J., Ankala, A., Gibson, K. M., Bowser, M., Sharma, H., Hynes, E. D., Hegde, M., Santani, A., Lebo, M. S., et al. (2016) · Genetics in Medicine · doi:10.1038/gim.2016.58 · Cited by 228
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Ball, M. P., Thakuria, J. V., Zaranek, A. W., Clegg, T., Rosenbaum, A. M., Wu, X., Angrist, M. H., Bhak, J., Bobe, J. R., Callow, M. J., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1201904109 · Cited by 224
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Self-citationOlson, N. D., Wagner, J., McDaniel, J., Stephens, S. H., Westreich, S. T., Prasanna, A. G., Johanson, E., Boja, E., Maier, E. J., Serang, O., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100129 · Cited by 202
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Regier, A., Farjoun, Y., Larson, D. E., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/269316 · Cited by 34
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Lennerz, J. K., Timmerman, R. J., Grange, D. K., DeBaun, M. R., Feinberg, A. P., & Zehnbauer, B. A. (2010) · Journal of Molecular Diagnostics · doi:10.2353/jmoldx.2010.100005 · Cited by 11
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- Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013). · arXiv
Cited by
Sorted by citations
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129
Self-citationA complete reference genome improves analysis of human genetic variation
Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., et al. (2022) · Science · doi:10.1126/science.abl3533 · Cited by 441
Self-citationPangenome graph construction from genome alignments with Minigraph-Cactus
Hickey, G., Monlong, J., Ebler, J., Novak, A. M., Eizenga, J. M., Gao, Y., Human Pangenome Reference Consortium, Abel, H. J., Antonacci-Fulton, L. L., Asri, M., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01793-w · Cited by 343
Self-citationEbler, J., Ebert, P., Clarke, W. E., Rausch, T., Audano, P. A., Houwaart, T., Mao, Y., Korbel, J. O., Eichler, E. E., Zody, M. C., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01043-w · Cited by 277
Self-citationSemi-automated assembly of high-quality diploid human reference genomes
Jarvis, E. D., Formenti, G., Rhie, A., Guarracino, A., Yang, C., Wood, J., Tracey, A., Thibaud-Nissen, F., Vollger, M. R., Porubsky, D., et al. (2022) · Nature · doi:10.1038/s41586-022-05325-5 · Cited by 209
Self-citationComprehensive genome analysis and variant detection at scale using DRAGEN
Behera, S., Catreux, S., Rossi, M., Truong, S., Huang, Z., Ruehle, M., Visvanath, A., Parnaby, G., Roddey, C., Onuchic, V., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02382-1 · Cited by 137
Self-citationAnalysis and benchmarking of small and large genomic variants across tandem repeats
English, A. C., Dolzhenko, E., Ziaei Jam, H., McKenzie, S. K., Olson, N. D., De Coster, W., Park, J., Gu, B., Wagner, J., Eberle, M. A., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02225-z · Cited by 68
Self-citationPangenome Graph Construction from Genome Alignment with Minigraph-Cactus
Hickey, G., Monlong, J., Ebler, J., Novak, A., Eizenga, J. M., Gao, Y., Human Pangenome Reference Consortium, Marschall, T., Li, H., & Paten, B. (2022) · doi:10.1101/2022.10.06.511217 · Cited by 345
Self-citationFixItFelix: improving genomic analysis by fixing reference errors
Behera, S., LeFaive, J., Orchard, P., Mahmoud, M., Paulin, L. F., Farek, J., Soto, D. C., Parker, S. C. J., Smith, A. V., Dennis, M. Y., et al. (2023) · Genome Biology · doi:10.1186/s13059-023-02863-7 · Cited by 28
Self-citation
Metadata
- Authors
- Wagner, J., Olson, N. D., Harris, L., McDaniel, J., Cheng, H., Fungtammasan, A., Hwang, Y.-C., Gupta, R., Wenger, A. M., Rowell, W. J., Khan, Z. M., Farek, J., Zhu, Y., Pisupati, A., Mahmoud, M., Xiao, C., Yoo, B., Sahraeian, S. M. E., Miller, D. E., Jáspez, D., Lorenzo-Salazar, J. M., Muñoz-Barrera, A., Rubio-Rodríguez, L. A., Flores, C., Narzisi, G., Evani, U. S., Clarke, W. E., Lee, J., Mason, C. E., Lincoln, S. E., Miga, K. H., Ebbert, M. T. W., Shumate, A., Li, H., Chin, C.-S., Zook, J. M., & Sedlazeck, F. J.
- Affiliations
- National Institute of Standards and Technology (US)
- Dana-Farber Cancer Institute (US)
- DNAnexus (United States) (US)
- Pacific Biosciences (United States) (US)
- Baylor College of Medicine (US)
- National Institutes of Health (US)
- Children's Mercy Hospital (US)
- Seattle Children's Hospital (US)
- Instituto Tecnológico y de Energías Renovables (ES)
- Instituto de Salud Carlos III (ES)
- New York Genome Center (US)
- BioNano Genomics (United States) (US)
- Weill Cornell Medicine (US)
- Invitae (United States) (US)
- University of California, Santa Cruz (US)
- University of Kentucky (US)
- Johns Hopkins University (US)
- Corresponding author
- Chin, Chen-Shan
- Zook, Justin M.
- Sedlazeck, Fritz J.
- ORCID
- Wagner, Justin
- Olson, Nathan D.
- Harris, Lindsay
- McDaniel, Jennifer
- Cheng, Haoyu
- Fungtammasan, Arkarachai
- Gupta, Richa
- Wenger, Aaron M.
- Rowell, William J.
- Khan, Ziad M.
- Farek, Jesse
- Zhu, Yiming
- Pisupati, Aishwarya
- Mahmoud, Medhat
- Xiao, Chunlin
- Yoo, Byunggil
- Miller, Danny E.
- Jáspez, David
- Lorenzo-Salazar, José M.
- Muñoz-Barrera, Adrián
- Rubio-Rodríguez, Luis A.
- Flores, Carlos
- Narzisi, Giuseppe
- Evani, Uday Shanker
- Clarke, Wayne E.
- Lee, Joyce
- Mason, Christopher E.
- Lincoln, Stephen E.
- Miga, Karen H.
- Ebbert, Mark T. W.
- Shumate, Alaina
- Li, Heng
- Chin, Chen-Shan
- Zook, Justin M.
- Sedlazeck, Fritz J.
- Venue
- Nature Biotechnology
- Published
- 2022-02-07
- Volume
- 40
- Issue
- 5
- Pages
- 672-680
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC9117392
- OpenAlex
- W4210887696
- Cited by
- 241
- References
- 81
- Citations by year
- 2026: 51 · 2025: 57 · 2024: 56 · 2023: 37 · 2022: 38
- FWCI
- 15.91
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Nature Biotechnology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Commons-TMC (Texas Medical Center) (submittedVersion)
- Funders
- United States Department of Commerce | National Institute of Standards and Technology (Intramural)
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (R01 HG010040, UM1 HG008898)
- U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (Intramural)
- Cabildo Insular de La Palma (BOC n.º 163, 24/08/2017)
- Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (PI20/00876)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- variant calling, indels, structural variants, CBS, CRYAA, KCNE1, Genome in a Bottle, HG002
- MeSH terms
- Haplotypes, Humans, Genome, Human, Sequence Analysis, DNA
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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