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Article: Sources of gene expression variation in a globally diverse human cohort.

Taylor, Dylan J / Chhetri, Surya B / Tassia, Michael G / Biddanda, Arjun / Battle, Alexis / McCoy, Rajiv C

bioRxiv : the preprint server for biology

2023

Abstract: Genetic variation influencing gene expression and splicing is a key source of phenotypic diversity. Though invaluable, studies investigating these links in humans have been strongly biased toward participants of European ancestries, diminishing ... ...

Abstract	Genetic variation influencing gene expression and splicing is a key source of phenotypic diversity. Though invaluable, studies investigating these links in humans have been strongly biased toward participants of European ancestries, diminishing generalizability and hindering evolutionary research. To address these limitations, we developed MAGE, an open-access RNA-seq data set of lymphoblastoid cell lines from 731 individuals from the 1000 Genomes Project spread across 5 continental groups and 26 populations. Most variation in gene expression (92%) and splicing (95%) was distributed within versus between populations, mirroring variation in DNA sequence. We mapped associations between genetic variants and expression and splicing of nearby genes (
Language	English
Publishing date	2023-11-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.04.565639
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.

Taylor, Dylan J / Eizenga, Jordan M / Li, Qiuhui / Das, Arun / Jenike, Katharine M / Kenny, Eimear E / Miga, Karen H / Monlong, Jean / McCoy, Rajiv C / Paten, Benedict / Schatz, Michael C

Annual review of genomics and human genetics

2024

Abstract: The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome reference sequence remained incomplete and lacked ... ...

Abstract	The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome reference sequence remained incomplete and lacked representation of human genetic diversity. Recently, two major advances have emerged to address these shortcomings: complete gap-free human genome sequences, such as the one developed by the Telomere-to-Telomere Consortium, and high-quality pangenomes, such as the one developed by the Human Pangenome Reference Consortium. Facilitated by advances in long-read DNA sequencing and genome assembly algorithms, complete human genome sequences resolve regions that have been historically difficult to sequence, including centromeres, telomeres, and segmental duplications. In parallel, pangenomes capture the extensive genetic diversity across populations worldwide. Together, these advances usher in a new era of genomics research, enhancing the accuracy of genomic analysis, paving the path for precision medicine, and contributing to deeper insights into human biology.
Language	English
Publishing date	2024-04-25
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2037670-4
ISSN	1545-293X ; 1527-8204
ISSN (online)	1545-293X
ISSN	1527-8204
DOI	10.1146/annurev-genom-021623-081639
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Article ; Online: Local adaptation and archaic introgression shape global diversity at human structural variant loci.

Yan, Stephanie M / Sherman, Rachel M / Taylor, Dylan J / Nair, Divya R / Bortvin, Andrew N / Schatz, Michael C / McCoy, Rajiv C

eLife

2021 Volume 10

Abstract: Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph- ... ...

Abstract	Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation - a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.
MeSH term(s)	Adaptation, Physiological/genetics ; Animals ; Asian People ; Evolution, Molecular ; Gene Flow ; Genome, Human ; Genomics ; Genotype ; Haplotypes/genetics ; Humans ; Linkage Disequilibrium ; Neanderthals/genetics ; Selection, Genetic
Language	English
Publishing date	2021-09-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.67615
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Article ; Online: Characterization of large-scale genomic differences in the first complete human genome.

Yang, Xiangyu / Wang, Xuankai / Zou, Yawen / Zhang, Shilong / Xia, Manying / Fu, Lianting / Vollger, Mitchell R / Chen, Nae-Chyun / Taylor, Dylan J / Harvey, William T / Logsdon, Glennis A / Meng, Dan / Shi, Junfeng / McCoy, Rajiv C / Schatz, Michael C / Li, Weidong / Eichler, Evan E / Lu, Qing / Mao, Yafei

Genome biology

2023 Volume 24, Issue 1, Page(s) 157

Abstract: Background: The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental duplication, and other complex ... ...

Abstract	Background: The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental duplication, and other complex regions. The current human genome reference (GRCh38) has been widely used in various human genomic studies. However, the large-scale genomic differences between these two important genome assemblies are not characterized in detail yet. Results: Here, in addition to the previously reported "non-syntenic" regions, we find 67 additional large-scale discrepant regions and precisely categorize them into four structural types with a newly developed website tool called SynPlotter. The discrepant regions (~ 21.6 Mbp) excluding telomeric and centromeric regions are highly structurally polymorphic in humans, where the deletions or duplications are likely associated with various human diseases, such as immune and neurodevelopmental disorders. The analyses of a newly identified discrepant region-the KLRC gene cluster-show that the depletion of KLRC2 by a single-deletion event is associated with natural killer cell differentiation in ~ 20% of humans. Meanwhile, the rapid amino acid replacements observed within KLRC3 are probably a result of natural selection in primate evolution. Conclusion: Our study provides a foundation for understanding the large-scale structural genomic differences between the two crucial human reference genomes, and is thereby important for future human genomics studies.
MeSH term(s)	Animals ; Humans ; Genome, Human ; Genomics ; Segmental Duplications, Genomic ; Multigene Family ; Centromere/genetics ; NK Cell Lectin-Like Receptor Subfamily C/genetics
Chemical Substances	KLRC2 protein, human ; NK Cell Lectin-Like Receptor Subfamily C
Language	English
Publishing date	2023-07-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-023-02995-w
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Article: Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes.

Xiang, Guanjue / He, Xi / Giardine, Belinda M / Isaac, Kathryn J / Taylor, Dylan J / McCoy, Rajiv C / Jansen, Camden / Keller, Cheryl A / Wixom, Alexander Q / Cockburn, April / Miller, Amber / Qi, Qian / He, Yanghua / Li, Yichao / Lichtenberg, Jens / Heuston, Elisabeth F / Anderson, Stacie M / Luan, Jing / Vermunt, Marit W /

Yue, Feng / Sauria, Michael E G / Schatz, Michael C / Taylor, James / Göttgens, Berthold / Hughes, Jim R / Higgs, Douglas R / Weiss, Mitchell J / Cheng, Yong / Blobel, Gerd A / Bodine, David M / Zhang, Yu / Li, Qunhua / Mahony, Shaun / Hardison, Ross C

bioRxiv : the preprint server for biology

2024

Abstract: Knowledge of locations and activities ... ...

Abstract	Knowledge of locations and activities of
Language	English
Publishing date	2024-03-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.04.02.535219
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Article: Utilization of single‐image normalized difference vegetation index (SI‐NDVI) for early plant stress detection

Beisel, Nicole S. / Callaham, Jordan B. / Sng, Natasha J. / Taylor, Dylan J. / Paul, Anna‐Lisa / Ferl, Robert J.

Applications in plant sciences. 2018 Oct., v. 6, no. 10

2018

Abstract: PREMISE OF THE STUDY: An imaging system was refined to monitor the health of vegetation grown in controlled conditions using spectral reflectance patterns. To measure plant health, the single‐image normalized difference vegetation index (SI‐NDVI) ... ...

Abstract	PREMISE OF THE STUDY: An imaging system was refined to monitor the health of vegetation grown in controlled conditions using spectral reflectance patterns. To measure plant health, the single‐image normalized difference vegetation index (SI‐NDVI) compares leaf reflectance in visible and near‐infrared light spectrums. METHODS AND RESULTS: The SI‐NDVI imaging system was characterized to assess plant responses to stress before visual detection during controlled stress assays. Images were analyzed using Fiji image processing software and Microsoft Excel to create qualitative false color images and quantitative graphs to detect plant stress. CONCLUSIONS: Stress was detected in Arabidopsis thaliana seedlings within 15 min of salinity application using SI‐NDVI analysis, before stress was visible. Stress was also observed during ammonium nitrate treatment of Eruca sativa plants before visual detection. Early detection of plant stress is possible using SI‐NDVI imaging, which is both simpler to use and more cost efficient than traditional dual‐image NDVI or hyper‐spectral imaging.
Keywords	Arabidopsis thaliana ; Eruca vesicaria subsp. sativa ; ammonium nitrate ; color ; computer software ; cost effectiveness ; leaf reflectance ; normalized difference vegetation index ; plant stress ; reflectance ; salinity ; vegetation ; Fiji
Language	English
Dates of publication	2018-10
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2699923-7
ISSN	2168-0450
ISSN	2168-0450
DOI	10.1002/aps3.1186
Database	NAL-Catalogue (AGRICOLA)

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Article: Utilization of single-image normalized difference vegetation index (SI-NDVI) for early plant stress detection.

Beisel, Nicole S / Callaham, Jordan B / Sng, Natasha J / Taylor, Dylan J / Paul, Anna-Lisa / Ferl, Robert J

Applications in plant sciences

2018 Volume 6, Issue 10, Page(s) e01186

Abstract: Premise of the study: An imaging system was refined to monitor the health of vegetation grown in controlled conditions using spectral reflectance patterns. To measure plant health, the single-image normalized difference vegetation index (SI-NDVI) ... ...

Abstract	Premise of the study: An imaging system was refined to monitor the health of vegetation grown in controlled conditions using spectral reflectance patterns. To measure plant health, the single-image normalized difference vegetation index (SI-NDVI) compares leaf reflectance in visible and near-infrared light spectrums. Methods and results: The SI-NDVI imaging system was characterized to assess plant responses to stress before visual detection during controlled stress assays. Images were analyzed using Fiji image processing software and Microsoft Excel to create qualitative false color images and quantitative graphs to detect plant stress. Conclusions: Stress was detected in
Language	English
Publishing date	2018-10-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2699923-7
ISSN	2168-0450
ISSN	2168-0450
DOI	10.1002/aps3.1186
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Article ; Online: A complete reference genome improves analysis of human genetic variation.

Aganezov, Sergey / Yan, Stephanie M / Soto, Daniela C / Kirsche, Melanie / Zarate, Samantha / Avdeyev, Pavel / Taylor, Dylan J / Shafin, Kishwar / Shumate, Alaina / Xiao, Chunlin / Wagner, Justin / McDaniel, Jennifer / Olson, Nathan D / Sauria, Michael E G / Vollger, Mitchell R / Rhie, Arang / Meredith, Melissa / Martin, Skylar / Lee, Joyce /

Koren, Sergey / Rosenfeld, Jeffrey A / Paten, Benedict / Layer, Ryan / Chin, Chen-Shan / Sedlazeck, Fritz J / Hansen, Nancy F / Miller, Danny E / Phillippy, Adam M / Miga, Karen H / McCoy, Rajiv C / Dennis, Megan Y / Zook, Justin M / Schatz, Michael C

Science (New York, N.Y.)

2022 Volume 376, Issue 6588, Page(s) eabl3533

Abstract: Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We ... ...

Abstract	Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics.
MeSH term(s)	Genetic Variation ; Genome, Human ; Genomics/standards ; Humans ; Reference Standards ; Sequence Analysis, DNA/standards
Language	English
Publishing date	2022-04-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abl3533
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Article ; Online: The complete sequence of a human Y chromosome.

Rhie, Arang / Nurk, Sergey / Cechova, Monika / Hoyt, Savannah J / Taylor, Dylan J / Altemose, Nicolas / Hook, Paul W / Koren, Sergey / Rautiainen, Mikko / Alexandrov, Ivan A / Allen, Jamie / Asri, Mobin / Bzikadze, Andrey V / Chen, Nae-Chyun / Chin, Chen-Shan / Diekhans, Mark / Flicek, Paul / Formenti, Giulio / Fungtammasan, Arkarachai /

Garcia Giron, Carlos / Garrison, Erik / Gershman, Ariel / Gerton, Jennifer L / Grady, Patrick G S / Guarracino, Andrea / Haggerty, Leanne / Halabian, Reza / Hansen, Nancy F / Harris, Robert / Hartley, Gabrielle A / Harvey, William T / Haukness, Marina / Heinz, Jakob / Hourlier, Thibaut / Hubley, Robert M / Hunt, Sarah E / Hwang, Stephen / Jain, Miten / Kesharwani, Rupesh K / Lewis, Alexandra P / Li, Heng / Logsdon, Glennis A / Lucas, Julian K / Makalowski, Wojciech / Markovic, Christopher / Martin, Fergal J / Mc Cartney, Ann M / McCoy, Rajiv C / McDaniel, Jennifer / McNulty, Brandy M / Medvedev, Paul / Mikheenko, Alla / Munson, Katherine M / Murphy, Terence D / Olsen, Hugh E / Olson, Nathan D / Paulin, Luis F / Porubsky, David / Potapova, Tamara / Ryabov, Fedor / Salzberg, Steven L / Sauria, Michael E G / Sedlazeck, Fritz J / Shafin, Kishwar / Shepelev, Valery A / Shumate, Alaina / Storer, Jessica M / Surapaneni, Likhitha / Taravella Oill, Angela M / Thibaud-Nissen, Françoise / Timp, Winston / Tomaszkiewicz, Marta / Vollger, Mitchell R / Walenz, Brian P / Watwood, Allison C / Weissensteiner, Matthias H / Wenger, Aaron M / Wilson, Melissa A / Zarate, Samantha / Zhu, Yiming / Zook, Justin M / Eichler, Evan E / O'Neill, Rachel J / Schatz, Michael C / Miga, Karen H / Makova, Kateryna D / Phillippy, Adam M

Nature

2023 Volume 621, Issue 7978, Page(s) 344–354

Abstract: The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental ... ...

Abstract	The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications
MeSH term(s)	Humans ; Base Sequence ; Chromosomes, Human, Y/genetics ; DNA, Satellite/genetics ; Genetic Variation/genetics ; Genetics, Population ; Genomics/methods ; Genomics/standards ; Heterochromatin/genetics ; Multigene Family/genetics ; Reference Standards ; Segmental Duplications, Genomic/genetics ; Sequence Analysis, DNA/standards ; Tandem Repeat Sequences/genetics ; Telomere/genetics
Chemical Substances	DNA, Satellite ; Heterochromatin ; TSPY1 protein, human ; RBMY1A1 protein, human ; DAZ1 protein, human
Language	English
Publishing date	2023-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-06457-y
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