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15. Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models

Author

Hynds, Robert E., Huebner, Ariana, Pearce, David R., Hill, Mark S., Akarca, Ayse U., Moore, David A., Ward, Sophia, Gowers, Kate H. C., Karasaki, Takahiro, Al Bakir, Maise, Wilson, Gareth A., Pich, Oriol, Martínez-Ruiz, Carlos, Hossain, A. S. Md Mukarram, Pearce, Simon P., Sivakumar, Monica, Ben Aissa, Assma, Grönroos, Eva, Chandrasekharan, Deepak, Kolluri, Krishna K., Towns, Rebecca, Wang, Kaiwen, Cook, Daniel E., Bosshard-Carter, Leticia, Naceur-Lombardelli, Cristina, Rowan, Andrew J., Veeriah, Selvaraju, Litchfield, Kevin, Crosbie, Philip A. J., Dive, Caroline, Quezada, Sergio A., Janes, Sam M., Jamal-Hanjani, Mariam, Marafioti, Teresa, McGranahan, Nicholas, and Swanton, Charles

Published
2024
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17. Cover

Author

Cook, Daniel Thomas

Published
2004

18. Bibliography

Author

Cook, Daniel Thomas

Published
2004

19. Index

Author

Cook, Daniel Thomas

Published
2004

21. Notes

Author

Cook, Daniel Thomas

Published
2004

31. The complete sequence and comparative analysis of ape sex chromosomes

Author

Makova, Kateryna D., Pickett, Brandon D., Harris, Robert S., Hartley, Gabrielle A., Cechova, Monika, Pal, Karol, Nurk, Sergey, Yoo, DongAhn, Li, Qiuhui, Hebbar, Prajna, McGrath, Barbara C., Antonacci, Francesca, Aubel, Margaux, Biddanda, Arjun, Borchers, Matthew, Bornberg-Bauer, Erich, Bouffard, Gerard G., Brooks, Shelise Y., Carbone, Lucia, Carrel, Laura, Carroll, Andrew, Chang, Pi-Chuan, Chin, Chen-Shan, Cook, Daniel E., Craig, Sarah J. C., de Gennaro, Luciana, Diekhans, Mark, Dutra, Amalia, Garcia, Gage H., Grady, Patrick G. S., Green, Richard E., Haddad, Diana, Hallast, Pille, Harvey, William T., Hickey, Glenn, Hillis, David A., Hoyt, Savannah J., Jeong, Hyeonsoo, Kamali, Kaivan, Pond, Sergei L. Kosakovsky, LaPolice, Troy M., Lee, Charles, Lewis, Alexandra P., Loh, Yong-Hwee E., Masterson, Patrick, McGarvey, Kelly M., McCoy, Rajiv C., Medvedev, Paul, Miga, Karen H., Munson, Katherine M., Pak, Evgenia, Paten, Benedict, Pinto, Brendan J., Potapova, Tamara, Rhie, Arang, Rocha, Joana L., Ryabov, Fedor, Ryder, Oliver A., Sacco, Samuel, Shafin, Kishwar, Shepelev, Valery A., Slon, Viviane, Solar, Steven J., Storer, Jessica M., Sudmant, Peter H., Sweetalana, Sweeten, Alex, Tassia, Michael G., Thibaud-Nissen, Françoise, Ventura, Mario, Wilson, Melissa A., Young, Alice C., Zeng, Huiqing, Zhang, Xinru, Szpiech, Zachary A., Huber, Christian D., Gerton, Jennifer L., Yi, Soojin V., Schatz, Michael C., Alexandrov, Ivan A., Koren, Sergey, O’Neill, Rachel J., Eichler, Evan E., and Phillippy, Adam M.

Published
2024
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39. A draft human pangenome reference

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K, Monlong, Jean, Abel, Haley J, Buonaiuto, Silvia, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M, Feng, Xiaowen, Fischer, Christian, Fulton, Robert S, Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T, Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J, Mitchell, Matthew W, Munson, Katherine M, Mwaniki, Moses Njagi, Novak, Adam M, Olsen, Hugh E, Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A, Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R, Antonacci-Fulton, Lucinda L, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Korbel, Jan O, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D, Popejoy, Alice B, Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A, Rhie, Arang, Sacco, Samuel, Sanders, Ashley D, Schneider, Valerie A, Schultz, Baergen I, Shafin, Kishwar, Smith, Michael W, Sofia, Heidi J, Abou Tayoun, Ahmad N, Thibaud-Nissen, Françoise, and Tricomi, Francesca Floriana

Subjects
Biological Sciences, Genetics, 2.1 Biological and endogenous factors, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Humans, Diploidy, Genome, Human, Haplotypes, Sequence Analysis, DNA, Genomics, Reference Standards, Cohort Studies, Alleles, Genetic Variation, General Science & Technology
Abstract

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Published
2023

40. Knowledge distillation for fast and accurate DNA sequence correction

Author

Belyaeva, Anastasiya, Shor, Joel, Cook, Daniel E., Shafin, Kishwar, Liu, Daniel, Töpfer, Armin, Wenger, Aaron M., Rowell, William J., Yang, Howard, Kolesnikov, Alexey, McLean, Cory Y., Nattestad, Maria, Carroll, Andrew, and Chang, Pi-Chuan

Subjects
Quantitative Biology - Genomics, Computer Science - Machine Learning
Abstract

Accurate genome sequencing can improve our understanding of biology and the genetic basis of disease. The standard approach for generating DNA sequences from PacBio instruments relies on HMM-based models. Here, we introduce Distilled DeepConsensus - a distilled transformer-encoder model for sequence correction, which improves upon the HMM-based methods with runtime constraints in mind. Distilled DeepConsensus is 1.3x faster and 1.5x smaller than its larger counterpart while improving the yield of high quality reads (Q30) over the HMM-based method by 1.69x (vs. 1.73x for larger model). With improved accuracy of genomic sequences, Distilled DeepConsensus improves downstream applications of genomic sequence analysis such as reducing variant calling errors by 39% (34% for larger model) and improving genome assembly quality by 3.8% (4.2% for larger model). We show that the representations learned by Distilled DeepConsensus are similar between faster and slower models.

Published
2022

41. Gaps and complex structurally variant loci in phased genome assemblies

Author

Porubsky, David, Vollger, Mitchell R, Harvey, William T, Rozanski, Allison N, Ebert, Peter, Hickey, Glenn, Hasenfeld, Patrick, Sanders, Ashley D, Stober, Catherine, Consortium, Human Pangenome Reference, Korbel, Jan O, Paten, Benedict, Marschall, Tobias, Eichler, Evan E, Abel, Haley J, Antonacci-Fulton, Lucinda L, Asri, Mobin, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Bourque, Guillaume, Buonaiuto, Silvia, Carroll, Andrew, Chaisson, Mark JP, Chang, Pi-Chuan, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Cody, Sarah, Colonna, Vincenza, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Doerr, Daniel, Ebler, Jana, Eizenga, Jordan M, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Feng, Xiaowen, Fischer, Christian, Flicek, Paul, Formenti, Giulio, Frankish, Adam, Fulton, Robert S, Gao, Yan, Garg, Shilpa, Garrison, Erik, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Groza, Cristian, Guarracino, Andrea, Haggerty, Leanne, Hall, Ira M, Haukness, Marina, Haussler, David, Heumos, Simon, Hoekzema, Kendra, Hourlier, Thibaut, Howe, Kerstin, Jain, Miten, Jarvis, Erich D, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Li, Heng, Liao, Wen-Wei, Lu, Shuangjia, Lu, Tsung-Yu, Lucas, Julian K, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, Markello, Charles, Martin, Fergal J, McCartney, Ann, McDaniel, Jennifer, Miga, Karen H, Mitchell, Matthew W, Monlong, Jean, Mountcastle, Jacquelyn, Munson, Katherine M, Mwaniki, Moses Njagi, Nattestad, Maria, Novak, Adam M, and Nurk, Sergey

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Humans, DNA, Satellite, Polymorphism, Genetic, Haplotypes, Segmental Duplications, Genomic, Sequence Analysis, DNA, Human Pangenome Reference Consortium, Medical and Health Sciences, Bioinformatics
Abstract

There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than 140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 182 haploid assemblies obtained from a diversity panel of 77 unique human samples. Although trio-based approaches using HiFi are the current gold standard, chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. Importantly, the majority of assembly gaps cluster near the largest and most identical repeats (including segmental duplications [35.4%], satellite DNA [22.3%], or regions enriched in GA/AT-rich DNA [27.4%]). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore, we estimate that 6-7 Mbp of DNA are misorientated per haplotype irrespective of whether trio-free or trio-based approaches are used. Of these misorientations, 81% correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large segmental duplications. We also identify large-scale alignment discontinuities consistent with 11.9 Mbp of deletions and 161.4 Mbp of insertions per haploid genome. Although 99% of this variation corresponds to satellite DNA, we identify 230 regions of euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Such variable and incompletely assembled regions are important targets for future algorithmic development and pangenome representation.

Published
2023

49. Introduction

Author

Sinanan, Kerry, Bautz, Annika, Cook, Daniel, Sinanan, Kerry, editor, Bautz, Annika, editor, and Cook, Daniel, editor

Published
2023
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