PreprintCited by 1,193Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalitiesGenomics and Rare Diseases

The DOI matches its Crossref record; 79 of the 79 references it cites were found in a registry or an index.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Open access

Schneider, Valerie A., Graves-Lindsay, Tina, Howe, Kerstin, Bouk, Nathan, Chen, Hsiu-Chuan, Kitts, Paul A., Murphy, Terence D., Pruitt, Kim D., Thibaud-Nissen, Françoise, Albracht, Derek, Fulton, Robert S., Kremitzki, Milinn, Magrini, Vincent, Markovic, Chris, McGrath, Sean, Steinberg, Karyn Meltz, Auger, Kate, Chow, William, Collins, Joanna, Harden, Glenn, Hubbard, Timothy, Pelan, Sarah, Simpson, Jared T., Threadgold, Glen, Torrance, James, Wood, Jonathan M., Clarke, Laura, Koren, Sergey, Boitano, Matthew, Peluso, Paul, Li, Heng, Chin, Chen-Shan, Phillippy, Adam M., Durbin, Richard, Wilson, Richard K., Flicek, Paul, Eichler, Evan E., Church, Deanna M.·2017·Genome Research

DOI 10.1101/gr.213611.116PMC PMC5411779

Published version of a preprint

Open this paper in CoChat — free account Open PDF

Abstract

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1101/gr.213611.116

Cites

79 of 79 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
Self-citation
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-citation
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEMPreprint
Li, H. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1303.3997 · Cited by 10,846
Self-citation
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Walker, 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
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
Self-citation
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
Self-citation
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357
Self-citation
A haplotype map of the human genome
The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEMPreprint
Li, H. (2014) · arXiv (Cornell University) · doi:10.6084/m9.figshare.963153.v1 · Cited by 5,155
Self-citation

Flagged first, then by citations

Show all 76 references

Sorted by citations

Items 901–999 of 999

Advancing the genetic utility of pre-clinical species through a high-quality assembly of the cynomolgus monkey ( Macaca fascicularis ) genomePreprint
Oziolor, E., Sullivan, S., Mangelson, H., Eacker, S. M., Agostino, M., Whiteley, L., Cook, J. C., & Koza-Taylor, P. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.01.072280
Template switching mechanism drives the tandem amplification of chromosome 20q11.21 in human pluripotent stem cellsPreprint
Halliwell, J. A., Baker, D., Judge, K., Quail, M. A., Oliver, K. L., Betteridge, E., Skelton, J., Andrews, P. W., & Barbaric, I. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.11.198382
Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine
Mahmoud, M., Gener, A. R., Khayat, M. M., English, A. C., Balaji, A., Zhou, A., Hehn, A., Fungtammasan, A., Chrisman, B., Chin, C.-S., et al. (2020) · F1000Research · doi:10.12688/f1000research.23773.1
Self-citation
Implications of Genetic Distance to Reference and De Novo Genome Assembly for Clinical Genomics in AfricansPreprint
Shriner, D., Adeyemo, A., & Rotimi, C. N. (2020) · medRxiv · doi:10.1101/2020.09.25.20201780
A High Quality Asian Genome Assembly Identifies Features of Common Missing Regions
Kim, J., Sung, J., Han, K., Lee, W., Mun, S., Lee, J., Bahk, K., Yang, I., Bae, Y.-K., Kim, C., et al. (2020) · Genes · doi:10.3390/genes11111350
The impact of post-alignment processing procedures on whole-exome sequencing data
Borges, M. G., de Moraes, H. T., Rocha, C. S., & Lopes‐Cendes, Í. (2020) · Genetics and Molecular Biology · doi:10.1590/1678-4685-gmb-2020-0047
Wild animal oral microbiomes reflect the history of human antibiotics usePreprint
Brealey, J. C., Leitão, H. G., Hofstede, T., Kalthoff, D. C., & Guschanski, K. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.22.423960
Homozygous and compound heterozygous rare variants in VPS13C contribute to Lewy body diseasesPreprint
Smolders, S., Philtjens, S., Crosiers, D., Sieben, A., Hens, E., Heeman, B., Mossevelde, S. V., Pals, P., Asselbergh, B., Dias, R. A., et al. (2020) · doi:10.21203/rs.3.rs-29975/v1
The landscape of high-affinity human antibodies against intratumoral antigensPreprint
Rakocevic, G., Glotova, I., de Santiago, I., Toptaş, B. Ç., Popovic, M., Popovic, M., Leone, D. A., Stachyra, A. L., Rozenfeld, R., Kural, D., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.06.430058
MaxDEL: Accurate and Efficient Calling Genomic Deletions From Single Molecular Real-Time Sequencing Using Integrated MethodPreprint
Lv, Y., Cai, L., & Gao, J. (2021) · Research Square · doi:10.21203/rs.3.rs-247574/v1
The Epigenome through the Lens of the Transcriptome and How it Regulates Tumour Development in Cancer
Reghbati, M. K. (2020) · TSpace (University of Toronto)
The Lithuanian reference genome LT1 - a human de novo genome assembly with short and long read sequence and Hi-C dataPreprint
Kim, H.-S., Blažytė, A., Jeon, S., Yoon, C., Kim, Y., Kim, C., Bolser, D. M., Ahn, J.-H., Edwards, J. S., & Bhak, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.05.438426 · Cited by 1
Peer Review #1 of "A total of 219 metagenome-assembled genomes of microorganisms from Icelandic marine waters (v0.1)"
(2021) · PeerJ · doi:10.7287/peerj.11112v0.1/reviews/1
Quantitation and Characterization of Cell-Free Mitochondrial DNA in Plasma by Deep SequencingPreprint
Daly, G. T., Pastukh, V. M., Tan, Y. B., Francis, C. M., Aggen, C. Z., Groark, S. C., Edwards, C., Hamo, M., Simmons, J. D., Kutcher, M., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-668341/v1
Investigation of parameters of chromatin higher order structure and the making of multiply-acetylated histone H3 via nonsense suppression
Young, I. A. (2021) · doi:10.31274/etd-20210609-204
GABOLA: A Reliable Gap-Filling Strategy for de novo Chromosome-Level AssemblyPreprint
Chuang, W., Cheng, H.-C. R., Chang, Y.-J., Fu, P.-Y., Huang, Y., Hsieha, P.-H., Chen, S., Lina, C.-Y., & Ho, J.-M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.07.459217
Genetic diversity and population structure within Botswana: association with HIV-1 infection
Thami, P. K. (2021) · Open University of Cape Town (University of Cape Town)
A Comparison of the Cellular and Molecular Atlases of the Macaque and Mouse Dorsal HornsPreprint
Arokiaraj, C. M., Kleyman, M., Chamessian, A. G., Shiers, S. I., Kang, B., Ng, M. M. K., Patterson, R., Lewis, D. A., Qadri, Y. J., Levine, A. J., et al. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3924596
[The esophageal cardiogram in several rheumatic heart diseases in children].
Garello, L. F., & GATTO, E. (1958) · PubMed
Peer Review #2 of "A total of 219 metagenome-assembled genomes of microorganisms from Icelandic marine waters (v0.1)"
(2021) · PeerJ · doi:10.7287/peerj.11112v0.1/reviews/2
THE VALUE OF PRIMARY TRANSCRIPTS TO THE CLINICAL AND NON-CLINICAL GENOMICS COMMUNITY: SURVEY RESULTS AND ROADMAP FOR IMPROVEMENTS. AUTHORSPreprint
Cunningham, F. M., Morales, J., McMahon, A., Loveland, J. E., Perry, E. H., Frankish, A., Hunt, S. E., Armean, I. M., & Flicek, P. (2021) · doi:10.22541/au.161901710.08079318/v1
Self-citation
Advances in Single Molecule, Real-Time (SMRT) Sequencing
Ameur, A., & Hestand, M. S. (2019) · MDPI eBooks · doi:10.3390/books978-3-03921-701-4
Real-Time Course: Reconstruction of cellular diversity and lineage trajectory based on somatic mutational patterns detected from low-pass single-cell transcriptome dataPreprint
Oota, S., Abe, K., Yokota, H., & Ikeo, K. (2022) · Research Square · doi:10.21203/rs.3.rs-1558242/v1
Faculty Opinions recommendation of Pan-genomics in the human genome era.
Mulder, N. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.737328554.793579953
Nomenclature
Iverson, C. (2020) · doi:10.1093/jama/9780190246556.003.0014
Faculty Opinions recommendation of Assembly of a pan-genome from deep sequencing of 910 humans of African descent.
Warren, S. T., & Garber, K. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734457663.793556112
Faculty Opinions recommendation of Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Tang, F. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.739619698.793585652
Faculty Opinions recommendation of Assembly of a pan-genome from deep sequencing of 910 humans of African descent.
Stankiewicz, P. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734457663.793554964
Response to Mitr and Pollack
Wickland, D. P., Sherman, M. E., Radisky, D. C., Mansfield, A. S., & Asmann, Y. W. (2022) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djac133
Perfil de expressão dos circRNAS no câncer colorretal
Freitas, V. G. (2022) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/d.95.2022.tde-12072022-110643
The Era of Genomic Research for Lymphoma: Looking Back and Forward
Chan, W. C., & Iqbal, J. (2022) · Hemato · doi:10.3390/hemato3030034
Comparison of an Oxford Nanopore Technologies Sequencing Platform to Existing Sequencing Methods for Differential Expression Studies
Klier, N. (2022) · doi:10.31979/etd.n6cs-f4jw
Dysfunctional B cell and interferon signaling in autoimmune polyendocrine syndrome type 1Preprint
Oftedal, B. E., Bruserud, Ø., Berger, A. H., Braun, S., Delaleu, N., Dolan, D., Røyrvik, E. C., Artaza, H., Meager, A., Husebye, E. S., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-2049437/v1
Digging into the Unknowns of the Human Genome Sequence: The T2T‐CHM13 Reference Assembly Release
Magrinelli, F., & Mencacci, N. E. (2022) · Movement Disorders · doi:10.1002/mds.29235
Genomic tools and models for investigating the role of germline diversity in mouse antibody repertoire development.
Kos, J. T. (2022) · doi:10.18297/etd/3825
Assessment of accuracy in identifying structural variants using third-generation sequencing for breast cancer in the absence of gold standardPreprint
Song, Q., Hu, T., Liang, B., Zhang, Z., Yang, L., Wu, J., Zhao, J. X., Long, M., Lian, S., Fan, X., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1970335/v1
Development and application of genetic ancestry reconstruction methods to study diversity of patient-derived models in the NCI PDXNet ConsortiumPreprint
Sanderson, B. J., Lott, P. C., Chiu, K., Quino, J. E., Vang, A. P., Lloyd, M. W., Srivastava, A., Chuang, J. H., & Carvajal‐Carmona, L. G. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.24.513591
Low-Cost Genome-Scale Phasing with Barcode-Linked Sequencing
Redin, D. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2819-5_6
The Human Genome
Gonzaga-Jauregui, C. G. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-822563-9.00085-8
Genomic and Proteomic Analysis of Patients with Reoccurring Discrete Subaortic StenosisPreprint
Birla, R. K., Singampalli, K. L., Nieuwsma, A., Brimmer, S., Kaul, A., Wadhwa, L., Jung, S. Y., Mezquita, D., Grimm, S. L., Balaji, S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.22.525022
Delineating genotypes and phenotypes of individual cells from long-read single cell transcriptomesPreprint
Shiau, C.-K., Lu, L., Kieser, R. E., Fukumura, K., Pan, T., Lin, H., Yang, J., Tong, E. L., Lee, G., Yan, Y., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.24.525264
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method
Yu, X., Lv, Y., Cai, L., & Gao, J. (2023) · Current Bioinformatics · doi:10.2174/1574893618666230224160716
Two-Cloud Private Read Alignment to a Public Reference Genome
Madabushi, S., & Ramanathan, P. (2023) · Proceedings on Privacy Enhancing Technologies · doi:10.56553/popets-2023-0062
Data from Phase II Clinical Trial of Eribulin–Gemcitabine Combination Therapy in Previously Treated Patients With Advanced Liposarcoma or Leiomyosarcoma
Kim, C. G., Sim, N. S., Kim, J. E., Yun, K., Lee, Y. H., Kim, S. H., Baek, W., Han, Y. D., Kim, S. K., Kim, J. H., et al. (2023) · doi:10.1158/1078-0432.c.6532644.v1
Data from Phase II Clinical Trial of Eribulin–Gemcitabine Combination Therapy in Previously Treated Patients With Advanced Liposarcoma or Leiomyosarcoma
Kim, C. G., Sim, N. S., Kim, J. E., Yun, K., Lee, Y. H., Kim, S. H., Baek, W., Han, Y. D., Kim, S. K., Kim, J. H., et al. (2023) · doi:10.1158/1078-0432.c.6532644
Gene panel analysis of literature-based infertility genes in Sertoli cell-only syndrome patients
Klarić, M. L., Žunić, L., Marić, T., Trgovec-Greif, L., Rokić, F., Merkler, A., Belužić, R., Vugrek, O., Bojanac, A. K., & Barbalić, M. (2023) · Genetics & Applications · doi:10.31383/ga.vol7iss1ga03
Clinically validated metatranscriptomic analysis of human and microbial components of FFPE tissue biopsiesPreprint
Toma, R., Hu, L., Demusaj, D., Mehrtash, M., Wohlman, R., Banavar, G. S., & Vuyisich, M. (2023) · medRxiv · doi:10.1101/2023.05.03.23289449
DNA Sequencing: The Future Perspective
Singh, K., Gupta, M. K., & Kumar, A. (2023) · Lecture notes in networks and systems · doi:10.1007/978-981-99-0483-9_14
Modification of the short read alignment algorithm to improve the quality of the human whole genome sequencing data processing pipeline
Guguchkin, E., & Karpulevich, E. (2023) · Proceedings of the Institute for System Programming of RAS · doi:10.15514/ispras-2023-35(2)-17
Improvement of selection criteria and prioritisation for neoantigen prediction
Pearngam, P. (2021) · doi:10.58837/chula.the.2021.16
Transformer-based modeling to study repetitive sequences of the human genome
Parejo, A. D. C., Seguel, J., & Ramos, K. S. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-824010-6.00059-9
Proyecto genoma veinte años después: el primer 'pangenoma humano'
Gamboa-Bernal, G. A. (2023) · Persona y Bioética · doi:10.5294/pebi.2023.27.2.1
De novo genome assemblies from two Indigenous Americans from Arizona identify new polymorphisms in non-reference sequencesPreprint
Köroğlu, Ç., Chen, P., Traurig, M. T., Altok, S., Bogardus, C., & Baier, L. J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.23.563520
Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversityPreprint
Chrisman, B., He, C., Jung, J.-Y., Stockham, N., Paskov, K. M., Washington, P. Y., Petereit, J., & Wall, D. P. (2023) · Genome Research · doi:10.1101/gr.277175.122
Comparative Analysis of Structural Variant Callers on Short-Read Whole-Genome Sequencing Data
Mkrtchyan, A. A., Grammatikati, K. S., Kazakova, P. G., Игоревич, М. С., Zemsky, P. U., Ивашечкин, А. А., Пилипенко, М. Н., Svetlichny, D. V., Sergeev, A. P., Snigir, E. A., et al. (2023) · Russian Journal of Genetics · doi:10.1134/s102279542306011x
Leveraging Complexity in Oncology – A Data Narrative
Briffaut, J., & Kourilsky, P. (2023) · Wiley eBooks · doi:10.1002/9781394255504.ch4
Determinants of plasma levels of gcg and metabolic impact of glucagon receptor signalling – a UK Biobank studyPreprint
Winther‐Sørensen, M., García, S. L., Bartholdy, A., Ottenheijm, M. E., Banasik, K., Brunak, S., Sørensen, C. M., Gluud, L. L., Knop, F. K., Holst, J. J., et al. (2023) · medRxiv · doi:10.1101/2023.12.12.23299852
Evaluation of Genome Conversion to Genome Reference Consortium Human Build 38 from Human Genome 19
Park, K., & Park, J.-H. (2023) · Imsang byeong'ri wa jeongdo gwanri/Journal of laboratory medicine and quality assurance · doi:10.15263/jlmqa.2023.45.4.180
Human pangenome: far-reaching implications in precision medicine
Yu, Y., & Chen, H. (2023) · Frontiers of Medicine · doi:10.1007/s11684-023-1039-1
Self-citation
GVRP: Genome Variant Refinement Pipeline for variant analysis in non-human species using machine learningPreprint
Choi, J., Zhou, B., & Song, G. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.14.575595
Main supplemental file from Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts
Moura, P. L., Blanco, T. M., Hofman, I. J., Todisco, G., Kretzschmar, W. W., Björklund, A.-C., Creignou, M., Hagemann-Jensen, M., Ziegenhain, C., Granados, D. C., et al. (2024) · doi:10.1158/0008-5472.25002166.v1
Main supplemental file from Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts
Moura, P. L., Blanco, T. M., Hofman, I. J., Todisco, G., Kretzschmar, W. W., Björklund, A.-C., Creignou, M., Hagemann-Jensen, M., Ziegenhain, C., Granados, D. C., et al. (2024) · doi:10.1158/0008-5472.25002166
Longest Order Conserved Repetition-free Subsequences
Zhang, S., Wang, Q., Zhu, D., & Jiang, H. (2023) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm58861.2023.10385586
Modeling platinum resistance in a stem-like patient-derived ovarian cancer samplePreprint
Suzuki, T., Conant, A., Jung, Y., Bax, R., Antonissen, A., Chen, W., Yu, G., Ioffe, Y., Wang, C., & Unternaehrer, J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.30.577975
Next-generation sequencing analysis with a population-specific reference genomePreprint
Suzuki, T., Ninomiya, K., Funayama, T., Okamura, Y., Tadaka, S., Kinoshita, K., Yamamoto, M. P., Kure, S., Kikuchi, A., Tamiya, G., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.07.584017
Additional file 2 of Increased prime edit rates in KCNQ2 and SCN1A via single nicking all-in-one plasmids
Dirkx, N., Weuring, W. J., Vriendt, E. D., Smal, N., van de Vondervoort, J., Slot, R. V. ‘., Koetsier, M. P., Zonnekein, N., Pooter, T. D., Weckhuysen, S., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23682255
SARS-CoV-2 disrupts host gene networks: unveiling key hub genes as potential therapeutic targets for COVID-19 managementPreprint
Marta, M., Maździarz, M. A., Krawczyk, K., Paukszto, Ł., Makowczenko, K. G., Lepiarczyk, E., Lipka, A., Wiszpolska, M., Górska, A., Moczulska, B., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4214583/v1
Comparative Analysis of Structural Variant Callers on the Short-Read Whole-Genome Sequencing Data
Mkrtchian, A. A., Grammatikati, K. S., Kazakova, P. G., Игоревич, М. С., Zemsky, P. U., Ивашечкин, А. А., Пилипенко, М. Н., Svetlichnyy, D. V., Sergeev, A., Snigir, E. A., et al. (2023) · Генетика · doi:10.31857/s0016675823060115
Genomic Feature of Filled Regions of Telomere-to-Telomere Genomes in Five Model SpeciesPreprint
Xiong, C., Zhang, H., Zhang, Y., Hao, L., Liang, Z., & Zheng, J. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4853623
The new epigenetic driver role of PPARα and mitochondria in metabolic dysfunction associated liver disease (MASLD), paving the way towards new therapeutics and diagnostic biomarkers
Theys, C. (2024) · doi:10.63028/10067/2022910151162165141
HLA Typing and Mutation Calling from Normal and Tumor Whole Genome Sequencing Data with ALPHLARD-NT
Hayashi, S., & Imoto, S. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3874-3_7
The potential of human leukocyte antigen alleles to assist with multiple-contributor DNA mixtures: Proof of concept study
Kuffel, A., Cole, C., Mallinder, B., Daéid, N. N., & Gray, A. (2024) · Science & Justice · doi:10.1016/j.scijus.2024.08.001
GENOMICON-Seq: A comprehensive tool for the simulation of mutations in amplicon and whole exome sequencingPreprint
Stosic, M. S., Costanzi, J., Ambur, O. H., & Rounge, T. B. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.14.607907
The first assembled chromosome-level genome of an individual from Karnataka, IndiaPreprint
Mhatre, A., Chindarkar, Y., Ganesh, A., Thakare, A., Mishra, P., Ravindran, F., Sharma, A., Srinivasan, S., & Choudhary, B. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.18.608448
Domestic freezer storage: a solution for preserving stool microbiota integrity for at-home collectionPreprint
Cabrera, P. M., Bokulich, N. A., & Zimmermann, P. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.02.610874
The Use of Next-Generation Sequencing in Diagnosing Inherited Atypical Parkinsonian Disorders
Chelban, V., Catereniuc, D., Groppa, S. A., & Houlden, H. (2024) · Neuromethods · doi:10.1007/978-1-0716-4083-8_9
Novel mechanism of inflammatory activation by Ebola virus matrix protein linked to the ebolavirus virulencePreprint
Yamaoka, S., Mhamdi, Z., Wang, L., Swenson, V. A., McNally, K. L., Lu, S., Singh, R., Saundh, S. L., Zell, B. N., Best, S. M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.06.616882
Next-generation sequencing analysis with a population-specific human reference genome
Suzuki, T., Ninomiya, K., Funayama, T., Okamura, Y., Tadaka, S., Kinoshita, K., Yamamoto, M. P., Kure, S., Kikuchi, A., Tamiya, G., et al. (2024) · Genes & Genetic Systems · doi:10.1266/ggs.24-00112
A review of neurogenetics in fetal and neonatal clinical medicine
Ananth, A., & Lopez, M. A. (2024) · Seminars in Fetal and Neonatal Medicine · doi:10.1016/j.siny.2024.101550
Augmenting transcriptome annotations through the lens of splicing evolutionPreprint
Zang, X. C., Chen, K., Khan, I. M., & Shao, M. (2026) · Genome Research · doi:10.1101/gr.280661.125
Analysis of gene expression in patients during acute cerebral insufficiency and late reconvalescence after severe neuroinfection
Александровна, И. А., Викторович, К. А., Скрипченко, Н. В., Vilnits, A. A., Alekseeva, L. A., Bessonova, T. V., Goleva, O. V., Марченко, Н. В., Irikova, M. A., Chukhlovin, A. B., et al. (2024) · CHILDREN INFECTIONS · doi:10.22627/2072-8107-2024-23-4-13-17
Genomic feature of filled regions of telomere-to-telomere genomes in five model speciesPreprint
Xiong, C., Zheng, J., Zhang, H., Zhang, Y., Hao, L., Wang, M., & Liang, Z. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.31.630859
Identification of Transdiagnostic Childhood Externalizing Pathology Within an Electronic Medical Records Database and Application to the Analysis of Rare Copy Number Variation
Reddy, I. A., Han, L., Sanchez‐Roige, S., Niarchou, M., Ruderfer, D. M., & Davis, L. K. (2025) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.33020 · Cited by 1
Microglia replacement by ER-Hoxb8 conditionally immortalized macrophages provides insight into Aicardi-Goutières Syndrome neuropathologyPreprint
Nemec, K. M., Uy, G., Chaluvadi, V. S., Purnell, F. S., Elfayoumi, B., O’Brien, C. A., Aisenberg, W. H., Lombroso, S. I., Guo, X., Blank, N., et al. (2025) · eLife · doi:10.7554/elife.102900.1
Weighted syncmer sampling improves long-read mapping
Quan, W., Kang, J., Deng, Y., Liu, Z., Zhu, X. G., & Quan, G. (2024) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm62325.2024.10821776
Ecological Trait Differences Are Associated with Gene Expression in the Primary Visual Cortex of Primates
Zintel, T. M., Ely, J. J., Raghanti, M. A., Hopkins, W. D., Hof, P. R., Sherwood, C. C., Kamilar, J. M., Bauernfeind, A. L., & Babbitt, C. C. (2025) · Genes · doi:10.3390/genes16020117
A Vectorized Sequence-to-Graph Alignment Algorithm
Peng, C., Tang, S., Guo, Y., Xia, Z., Yang, C., & Cui, Y. (2025) · Lecture notes in computer science · doi:10.1007/978-981-96-1525-4_22
BLASTing Forensic PCR Primers
Wünschiers, R. (2025) · Springer eBooks · doi:10.1007/978-3-031-70314-0_18
Preparation of robust synthetic control samples and their use in a metatranscriptomic clinical test
Toma, R., Hu, L., Banavar, G. S., & Vuyisich, M. (2025) · Scientific Reports · doi:10.1038/s41598-025-95020-y
Genetics as a Natural Resource
McCormack, K., & Torres, J. B. (2025) · doi:10.1093/9780198945246.003.0058
Predicting Nonsense-mediated mRNA Decay from Splicing Events in Sepsis using RNA-Sequencing DataPreprint
Shin, J., Fredericks, A. M., Armstead, B. E., Ayala, A., Cohen, M., Fairbrother, W. G., Levy, M. M., Lillard, K. K., Raggi, E., Nau, G. J., et al. (2025) · medRxiv · doi:10.1101/2025.03.31.25324958
De novo assembly of plasmodium interspersed repeat (pir) genes from Plasmodium vivax RNAseq data suggests geographic conservation of sub-family transcriptionPreprint
Little, T. S., Cunningham, D., Christophides, G. K., Reid, A. J., & Langhorne, J. (2025) · Research Square · doi:10.21203/rs.3.rs-5822769/v1
Lossless pangenome indexing using tag arrays
Eskandar, P., Paten, B., & Sirén, J. (2026) · Algorithms for Molecular Biology · doi:10.1186/s13015-026-00301-4 · Cited by 1
Assembling unmapped reads reveals hidden variation in South Asian genomes
Das, A., Biddanda, A., McCoy, R. C., & Schatz, M. C. (2026) · Nature Communications · doi:10.1038/s41467-026-71755-8
Neurogenetics in the Genome Era
Chen, W.-L., Gropman, A. L., & Dobyns, W. B. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-10944-7.00048-2
Microglia replacement by ER-Hoxb8 conditionally immortalized macrophages provides insight into Aicardi-Goutières Syndrome neuropathologyPreprint
Nemec, K. M., Uy, G., Chaluvadi, V. S., Purnell, F. S., Elfayoumi, B., Byerly, L., O’Reilly, M. L., O’Brien, C. A., Aisenberg, W. H., Lombroso, S. I., et al. (2025) · eLife · doi:10.7554/elife.102900.2
Toward success in omics studies
Izard, J. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-22376-1.00005-2
Beating Transformers Using Synthetic Cognition
Ibias, A., Rodriguez-Galindo, M., Antona, H., Ramirez-Miranda, G., & Guinovart, E. (2025) · Lecture notes in computer science · doi:10.1007/978-3-032-00686-8_26
Inference of Genetic Ancestry from Cancer-Derived Molecular Data with RAIDS
Belleau, P., Deschênes, A., Tuveson, D. A., & Krasnitz, A. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4566-6_8

Authors: Schneider, V. A., Graves-Lindsay, T., Howe, K., Bouk, N., Chen, H.-C., Kitts, P. A., Murphy, T. D., Pruitt, K. D., Thibaud-Nissen, F., Albracht, D., Fulton, R. S., Kremitzki, M., Magrini, V., Markovic, C., McGrath, S., Steinberg, K. M., Auger, K., Chow, W., Collins, J., Harden, G., Hubbard, T., Pelan, S., Simpson, J. T., Threadgold, G., Torrance, J., Wood, J. M., Clarke, L., Koren, S., Boitano, M., Peluso, P., Li, H., Chin, C.-S., Phillippy, A. M., Durbin, R., Wilson, R. K., Flicek, P., Eichler, E. E., & Church, D. M.
Affiliations: Washington University in St. Louis (US)
Wellcome Sanger Institute (GB)
National Institutes of Health (US)
European Bioinformatics Institute (GB)
Pacific Biosciences (United States) (US)
Broad Institute (US)
Howard Hughes Medical Institute (US)
ORCID: Graves-Lindsay, Tina
Howe, Kerstin
Murphy, Terence D.
Pruitt, Kim D.
Fulton, Robert S.
Kremitzki, Milinn
Magrini, Vincent
McGrath, Sean
Steinberg, Karyn Meltz
Chow, William
Collins, Joanna
Pelan, Sarah
Simpson, Jared T.
Threadgold, Glen
Torrance, James
Wood, Jonathan M.
Clarke, Laura
Koren, Sergey
Peluso, Paul
Li, Heng
Chin, Chen-Shan
Phillippy, Adam M.
Durbin, Richard
Wilson, Richard K.
Flicek, Paul
Eichler, Evan E.
Church, Deanna M.
Venue: Genome Research
Publisher: Cold Spring Harbor Laboratory
Published: 2017-04-10
Volume: 27
Issue: 5
Pages: 849-864
ISSN: 1088-9051 (ISSN-L)
1549-5469
DOI: 10.1101/gr.213611.116
PMC: PMC5411779
OpenAlex: W2953263404
Cited by: 1,193
References: 76
Citations by year: 2026: 146 · 2025: 185 · 2024: 177 · 2023: 156 · 2022: 152 · 2021: 127 · 2020: 92 · 2019: 83 · 2018: 54 · 2017: 18
Type: posted content
Language: en
Open access: bronze
doi.org
Locations: Genome Research (publishedVersion)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Digital Commons@Becker (Washington University School of Medicine) (submittedVersion)
Research Portal (King's College London) (submittedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: National Institutes of Health (5U54HG003079, 5U41HG007635, HG002385, HG007635)
National Library of Medicine
Wellcome Trust (WT095908, WT098051, WT104947/Z/14/Z)
European Molecular Biology Laboratory
National Human Genome Research Institute
Howard Hughes Medical Institute
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Keywords: GRCh38, long-read sequencing, centromere, population genetic variation, variant interpretation, read mapping, assembly quality evaluation
MeSH terms: Haploidy, Haplotypes, Humans, Polymorphism, Genetic, Reference Standards, Software, Genome, Human, Sequence Analysis, DNA, Contig Mapping, Genomics

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 ›

Are you an author, or do you see a problem with this page? Request a review

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks