201
|
Seoighe C, Scally A. Inference of Candidate Germline Mutator Loci in Humans from Genome-Wide Haplotype Data. PLoS Genet 2017; 13:e1006549. [PMID: 28095480 PMCID: PMC5283766 DOI: 10.1371/journal.pgen.1006549] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 01/31/2017] [Accepted: 12/20/2016] [Indexed: 12/27/2022] Open
Abstract
The rate of germline mutation varies widely between species but little is known about the extent of variation in the germline mutation rate between individuals of the same species. Here we demonstrate that an allele that increases the rate of germline mutation can result in a distinctive signature in the genomic region linked to the affected locus, characterized by a number of haplotypes with a locally high proportion of derived alleles, against a background of haplotypes carrying a typical proportion of derived alleles. We searched for this signature in human haplotype data from phase 3 of the 1000 Genomes Project and report a number of candidate mutator loci, several of which are located close to or within genes involved in DNA repair or the DNA damage response. To investigate whether mutator alleles remained active at any of these loci, we used de novo mutation counts from human parent-offspring trios in the 1000 Genomes and Genome of the Netherlands cohorts, looking for an elevated number of de novo mutations in the offspring of parents carrying a candidate mutator haplotype at each of these loci. We found some support for two of the candidate loci, including one locus just upstream of the BRSK2 gene, which is expressed in the testis and has been reported to be involved in the response to DNA damage.
Collapse
Affiliation(s)
- Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, NUI Galway, Galway, Ireland
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
202
|
Zhu YO, Sherlock G, Petrov DA. Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum. PLoS Genet 2017; 13:e1006455. [PMID: 28046117 PMCID: PMC5207638 DOI: 10.1371/journal.pgen.1006455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 11/03/2016] [Indexed: 12/04/2022] Open
Abstract
The characterization of mutational spectra is usually carried out in one of three ways-by direct observation through mutation accumulation (MA) experiments, through parent-offspring sequencing, or by indirect inference from sequence data. Direct observations of spontaneous mutations with MA experiments are limited, given (i) the rarity of spontaneous mutations, (ii) applicability only to laboratory model species with short generation times, and (iii) the possibility that mutational spectra under lab conditions might be different from those observed in nature. Trio sequencing is an elegant solution, but it is not applicable in all organisms. Indirect inference, usually from divergence data, faces no such technical limitations, but rely upon critical assumptions regarding the strength of natural selection that are likely to be violated. Ideally, new mutational events would be directly observed before the biased filter of selection, and without the technical limitations common to lab experiments. One approach is to identify very young mutations from population sequencing data. Here we do so by leveraging two characteristics common to all new mutations-new mutations are necessarily rare in the population, and absent in the genomes of immediate relatives. From 132 clinical yeast strains, we were able to identify 1,425 putatively new mutations and show that they exhibit extremely low signatures of selection, as well as display a mutational spectrum that is similar to that identified by a large scale MA experiment. We verify that population sequencing data are a potential wealth of information for inferring mutational spectra, and should be considered for analysis where MA experiments are infeasible or especially tedious.
Collapse
Affiliation(s)
- Yuan O. Zhu
- Department of Genetics, Stanford University, Stanford, CA, United States of America
- Department of Biology, Stanford University, Stanford, CA, United States of America
- Genome Institute of Singapore, Singapore
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA, United States of America
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA, United States of America
| |
Collapse
|
203
|
Zastrow DB, Zornio PA, Dries A, Kohler J, Fernandez L, Waggott D, Walkiewicz M, Eng CM, Manning MA, Farrelly E, Fisher PG, Ashley EA, Bernstein JA, Wheeler MT. Exome sequencing identifies de novo pathogenic variants in FBN1 and TRPS1 in a patient with a complex connective tissue phenotype. Cold Spring Harb Mol Case Stud 2017; 3:a001388. [PMID: 28050602 PMCID: PMC5171698 DOI: 10.1101/mcs.a001388] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/20/2016] [Indexed: 11/24/2022] Open
Abstract
Here we describe a patient who presented with a history of congenital diaphragmatic hernia, inguinal hernia, and recurrent umbilical hernia. She also has joint laxity, hypotonia, and dysmorphic features. A unifying diagnosis was not identified based on her clinical phenotype. As part of her evaluation through the Undiagnosed Diseases Network, trio whole-exome sequencing was performed. Pathogenic variants in FBN1 and TRPS1 were identified as causing two distinct autosomal dominant conditions, each with de novo inheritance. Fibrillin 1 (FBN1) mutations are associated with Marfan syndrome and a spectrum of similar phenotypes. TRPS1 mutations are associated with trichorhinophalangeal syndrome types I and III. Features of both conditions are evident in the patient reported here. Discrepant features of the conditions (e.g., stature) and the young age of the patient may have made a clinical diagnosis more difficult in the absence of exome-wide genetic testing.
Collapse
Affiliation(s)
- Diane B Zastrow
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Division of Cardiovascular Medicine, Stanford University, Stanford, California 94305, USA
| | - Patricia A Zornio
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Division of Cardiovascular Medicine, Stanford University, Stanford, California 94305, USA
| | - Annika Dries
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Division of Cardiovascular Medicine, Stanford University, Stanford, California 94305, USA
| | - Jennefer Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Division of Cardiovascular Medicine, Stanford University, Stanford, California 94305, USA
| | - Liliana Fernandez
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Division of Cardiovascular Medicine, Stanford University, Stanford, California 94305, USA
| | - Daryl Waggott
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Division of Cardiovascular Medicine, Stanford University, Stanford, California 94305, USA
| | | | - Christine M Eng
- Baylor Miraca Genetics Laboratories, Houston, Texas 77021-2024, USA
| | - Melanie A Manning
- Department of Pathology, Stanford School of Medicine, Stanford, California 94305, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, California 94305, USA
| | - Ellyn Farrelly
- Lucille Packard Children's Hospital Stanford, Palo Alto, California 94304, USA
| | - Paul G Fisher
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, California 94305, USA
- Department of Neurology, Stanford School of Medicine, Stanford, California 94304, USA
| | - Euan A Ashley
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Division of Cardiovascular Medicine, Stanford University, Stanford, California 94305, USA
- Department of Genetics, Stanford School of Medicine, Stanford, California 94305, USA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, California 94305, USA
- Lucille Packard Children's Hospital Stanford, Palo Alto, California 94304, USA
| | - Matthew T Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California 94305, USA
- Division of Cardiovascular Medicine, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
204
|
Statistical Methods for Identifying Sequence Motifs Affecting Point Mutations. Genetics 2016; 205:843-856. [PMID: 27974498 DOI: 10.1534/genetics.116.195677] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/01/2016] [Indexed: 11/18/2022] Open
Abstract
Mutation processes differ between types of point mutation, genomic locations, cells, and biological species. For some point mutations, specific neighboring bases are known to be mechanistically influential. Beyond these cases, numerous questions remain unresolved, including: what are the sequence motifs that affect point mutations? How large are the motifs? Are they strand symmetric? And, do they vary between samples? We present new log-linear models that allow explicit examination of these questions, along with sequence logo style visualization to enable identifying specific motifs. We demonstrate the performance of these methods by analyzing mutation processes in human germline and malignant melanoma. We recapitulate the known CpG effect, and identify novel motifs, including a highly significant motif associated with A[Formula: see text]G mutations. We show that major effects of neighbors on germline mutation lie within [Formula: see text] of the mutating base. Models are also presented for contrasting the entire mutation spectra (the distribution of the different point mutations). We show the spectra vary significantly between autosomes and X-chromosome, with a difference in T[Formula: see text]C transition dominating. Analyses of malignant melanoma confirmed reported characteristic features of this cancer, including statistically significant strand asymmetry, and markedly different neighboring influences. The methods we present are made freely available as a Python library https://bitbucket.org/pycogent3/mutationmotif.
Collapse
|
205
|
Seplyarskiy VB, Andrianova MA, Bazykin GA. APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW context. Genome Res 2016; 27:175-184. [PMID: 27940951 PMCID: PMC5287224 DOI: 10.1101/gr.210336.116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 12/01/2016] [Indexed: 12/18/2022]
Abstract
APOBEC3A/B cytidine deaminase is responsible for the majority of cancerous mutations in a large fraction of cancer samples. However, its role in heritable mutagenesis remains very poorly understood. Recent studies have demonstrated that both in yeast and in human cancerous cells, most APOBEC3A/B-induced mutations occur on the lagging strand during replication and on the nontemplate strand of transcribed regions. Here, we use data on rare human polymorphisms, interspecies divergence, and de novo mutations to study germline mutagenesis and to analyze mutations at nucleotide contexts prone to attack by APOBEC3A/B. We show that such mutations occur preferentially on the lagging strand and on nontemplate strands of transcribed regions. Moreover, we demonstrate that APOBEC3A/B-like mutations tend to produce strand-coordinated clusters, which are also biased toward the lagging strand. Finally, we show that the mutation rate is increased 3' of C→G mutations to a greater extent than 3' of C→T mutations, suggesting pervasive trans-lesion bypass of the APOBEC3A/B-induced damage. Our study demonstrates that 20% of C→T and C→G mutations in the TpCpW context-where W denotes A or T, segregating as polymorphisms in human population-or 1.4% of all heritable mutations are attributable to APOBEC3A/B activity.
Collapse
Affiliation(s)
- Vladimir B Seplyarskiy
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127994, Russia.,Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Maria A Andrianova
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127994, Russia.,Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Lomonosov Moscow State University, Moscow 119234, Russia
| | - Georgii A Bazykin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127994, Russia.,Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Lomonosov Moscow State University, Moscow 119234, Russia.,Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia
| |
Collapse
|
206
|
Harpak A, Bhaskar A, Pritchard JK. Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans. PLoS Genet 2016; 12:e1006489. [PMID: 27977673 PMCID: PMC5157949 DOI: 10.1371/journal.pgen.1006489] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/16/2016] [Indexed: 01/06/2023] Open
Abstract
The site frequency spectrum (SFS) has long been used to study demographic history and natural selection. Here, we extend this summary by examining the SFS conditional on the alleles found at the same site in other species. We refer to this extension as the "phylogenetically-conditioned SFS" or cSFS. Using recent large-sample data from the Exome Aggregation Consortium (ExAC), combined with primate genome sequences, we find that human variants that occurred independently in closely related primate lineages are at higher frequencies in humans than variants with parallel substitutions in more distant primates. We show that this effect is largely due to sites with elevated mutation rates causing significant departures from the widely-used infinite sites mutation model. Our analysis also suggests substantial variation in mutation rates even among mutations involving the same nucleotide changes. In summary, we show that variable mutation rates are key determinants of the SFS in humans.
Collapse
Affiliation(s)
- Arbel Harpak
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Anand Bhaskar
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
| | - Jonathan K. Pritchard
- Department of Biology, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
| |
Collapse
|
207
|
Acuna-Hidalgo R, Veltman JA, Hoischen A. New insights into the generation and role of de novo mutations in health and disease. Genome Biol 2016; 17:241. [PMID: 27894357 PMCID: PMC5125044 DOI: 10.1186/s13059-016-1110-1] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases. In fact, the occurrence of novel mutations in each generation explains why these reproductively lethal disorders continue to occur in our population. Recent studies have also shown that de novo mutations are predominantly of paternal origin and that their number increases with advanced paternal age. Here, we review the recent literature on de novo mutations, covering their detection, biological characterization, and medical impact.
Collapse
Affiliation(s)
- Rocio Acuna-Hidalgo
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
- Department of Clinical Genetics, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Alexander Hoischen
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| |
Collapse
|
208
|
Poot M. When Recessive Genes Mutate to Dominant Gene Action. Mol Syndromol 2016; 7:249-250. [PMID: 27867339 DOI: 10.1159/000449116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2016] [Indexed: 11/19/2022] Open
|
209
|
Besenbacher S, Sulem P, Helgason A, Helgason H, Kristjansson H, Jonasdottir A, Jonasdottir A, Magnusson OT, Thorsteinsdottir U, Masson G, Kong A, Gudbjartsson DF, Stefansson K. Multi-nucleotide de novo Mutations in Humans. PLoS Genet 2016; 12:e1006315. [PMID: 27846220 PMCID: PMC5147774 DOI: 10.1371/journal.pgen.1006315] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 08/22/2016] [Indexed: 01/23/2023] Open
Abstract
Mutation of the DNA molecule is one of the most fundamental processes in biology. In this study, we use 283 parent-offspring trios to estimate the rate of mutation for both single nucleotide variants (SNVs) and short length variants (indels) in humans and examine the mutation process. We found 17812 SNVs, corresponding to a mutation rate of 1.29 × 10-8 per position per generation (PPPG) and 1282 indels corresponding to a rate of 9.29 × 10-10 PPPG. We estimate that around 3% of human de novo SNVs are part of a multi-nucleotide mutation (MNM), with 558 (3.1%) of mutations positioned less than 20kb from another mutation in the same individual (median distance of 525bp). The rate of de novo mutations is greater in late replicating regions (p = 8.29 × 10-19) and nearer recombination events (p = 0.0038) than elsewhere in the genome.
Collapse
Affiliation(s)
| | | | - Agnar Helgason
- deCODE genetics/Amgen, Inc., Iceland.,Department of Anthropology, University of Iceland, Iceland
| | - Hannes Helgason
- deCODE genetics/Amgen, Inc., Iceland.,School of Engineering and Natural Sciences, University of Iceland, Iceland
| | | | | | | | | | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Iceland.,Faculty of Medicine, University of Iceland, Iceland
| | | | | | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Iceland.,School of Engineering and Natural Sciences, University of Iceland, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Iceland.,Faculty of Medicine, University of Iceland, Iceland
| |
Collapse
|
210
|
Jiang Y, Li Z, Liu Z, Chen D, Wu W, Du Y, Ji L, Jin ZB, Li W, Wu J. mirDNMR: a gene-centered database of background de novo mutation rates in human. Nucleic Acids Res 2016; 45:D796-D803. [PMID: 27799474 PMCID: PMC5210538 DOI: 10.1093/nar/gkw1044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 09/29/2016] [Accepted: 10/22/2016] [Indexed: 01/24/2023] Open
Abstract
De novo germline mutations (DNMs) are the rarest genetic variants proven to cause a considerable number of sporadic genetic diseases, such as autism spectrum disorders, epileptic encephalopathy, schizophrenia, congenital heart disease, type 1 diabetes, and hearing loss. However, it is difficult to accurately assess the cause of DNMs and identify disease-causing genes from the considerable number of DNMs in probands. A common method to this problem is to identify genes that harbor significantly more DNMs than expected by chance, with accurate background DNM rate (DNMR) required. Therefore, in this study, we developed a novel database named mirDNMR for the collection of gene-centered background DNMRs obtained from different methods and population variation data. The database has the following functions: (i) browse and search the background DNMRs of each gene predicted by four different methods, including GC content (DNMR-GC), sequence context (DNMR-SC), multiple factors (DNMR-MF) and local DNA methylation level (DNMR-DM); (ii) search variant frequencies in publicly available databases, including ExAC, ESP6500, UK10K, 1000G and dbSNP and (iii) investigate the DNM burden to prioritize candidate genes based on the four background DNMRs using three statistical methods (TADA, Binomial and Poisson test). As a case study, we successfully employed our database in candidate gene prioritization for a sporadic complex disease: intellectual disability. In conclusion, mirDNMR (https://www.wzgenomics.cn/mirdnmr/) can be widely used to identify the genetic basis of sporadic genetic diseases.
Collapse
Affiliation(s)
- Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Denghui Chen
- Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Wanying Wu
- Beijing Institutes of Life Science, Chinese Academy of Science, Beijing 100101, China
| | - Yaoqiang Du
- Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Liying Ji
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Zi-Bing Jin
- The Eye Hospital of Wenzhou Medical University, The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health, Wenzhou 325000, China
| | - Wei Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| |
Collapse
|
211
|
Abstract
Our understanding of the chronology of human evolution relies on the “molecular clock” provided by the steady accumulation of substitutions on an evolutionary lineage. Recent analyses of human pedigrees have called this understanding into question by revealing unexpectedly low germline mutation rates, which imply that substitutions accrue more slowly than previously believed. Translating mutation rates estimated from pedigrees into substitution rates is not as straightforward as it may seem, however. We dissect the steps involved, emphasizing that dating evolutionary events requires not “a mutation rate” but a precise characterization of how mutations accumulate in development in males and females—knowledge that remains elusive.
Collapse
Affiliation(s)
- Priya Moorjani
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- * E-mail: (PM); (ZG); (MP)
| | - Ziyue Gao
- Howard Hughes Medical Institute & Dept. of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail: (PM); (ZG); (MP)
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- * E-mail: (PM); (ZG); (MP)
| |
Collapse
|
212
|
Chen IC, Hernandez C, Xu X, Cooney A, Wang Y, McCarrey JR. Dynamic Variations in Genetic Integrity Accompany Changes in Cell Fate. Stem Cells Dev 2016; 25:1698-1708. [PMID: 27627671 DOI: 10.1089/scd.2016.0221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pluripotent stem cells hold the potential to form the basis of novel approaches to treatment of disease in vivo as well as to facilitate the generation of models for human disease, providing powerful avenues to discovery of novel diagnostic biomarkers and/or innovative drug regimens in vitro. However, this will require extensive maintenance, expansion, and manipulation of these cells in culture, which raises a concern regarding the extent to which genetic integrity will be preserved throughout these manipulations. We used a mutation reporter (lacI) transgene approach to conduct direct comparisons of mutation frequencies in cell populations that shared a common origin and genetic identity, but were induced to undergo transitions in cell fate between pluripotent and differentiated states, or vice versa. We confirm that pluripotent cells normally maintain enhanced genetic integrity relative to that in differentiated cells, and we extend this finding to show that dynamic transformations in the relative stringency at which genetic integrity is maintained are associated with transitions between pluripotent and differentiated cellular states. These results provide insight into basic biological distinctions between pluripotent and differentiated cell types that impact genetic integrity in a manner that is directly relevant to the potential clinical use of these cell types.
Collapse
Affiliation(s)
- I-Chung Chen
- 1 Department of Biology, University of Texas at San Antonio , San Antonio, Texas
| | - Christine Hernandez
- 1 Department of Biology, University of Texas at San Antonio , San Antonio, Texas
| | - Xueping Xu
- 2 Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center , Houston, Texas
| | - Austin Cooney
- 2 Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center , Houston, Texas.,3 Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell , Medical School, Austin, Texas
| | - Yufeng Wang
- 1 Department of Biology, University of Texas at San Antonio , San Antonio, Texas
| | - John R McCarrey
- 1 Department of Biology, University of Texas at San Antonio , San Antonio, Texas
| |
Collapse
|
213
|
Mao Q, Ciotlos S, Zhang RY, Ball MP, Chin R, Carnevali P, Barua N, Nguyen S, Agarwal MR, Clegg T, Connelly A, Vandewege W, Zaranek AW, Estep PW, Church GM, Drmanac R, Peters BA. The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes. Gigascience 2016; 5:42. [PMID: 27724973 PMCID: PMC5057367 DOI: 10.1186/s13742-016-0148-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/19/2016] [Indexed: 02/01/2023] Open
Abstract
Background Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. Findings As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics’ Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics’ standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data. Conclusions These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function. Electronic supplementary material The online version of this article (doi:10.1186/s13742-016-0148-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Qing Mao
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA
| | - Serban Ciotlos
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA
| | - Rebecca Yu Zhang
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA
| | - Madeleine P Ball
- Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,PersonalGenomes.org, 423 Brookline Avenue, #323, Boston, MA, 02215, USA
| | - Robert Chin
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA
| | - Paolo Carnevali
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA
| | - Nina Barua
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA
| | - Staci Nguyen
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA
| | - Misha R Agarwal
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA
| | - Tom Clegg
- Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Curoverse Inc., 212 Elm St, 3rd Floor, Somerville, MA, 02144, USA
| | - Abram Connelly
- Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Curoverse Inc., 212 Elm St, 3rd Floor, Somerville, MA, 02144, USA
| | - Ward Vandewege
- Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Curoverse Inc., 212 Elm St, 3rd Floor, Somerville, MA, 02144, USA
| | - Alexander Wait Zaranek
- Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Curoverse Inc., 212 Elm St, 3rd Floor, Somerville, MA, 02144, USA
| | - Preston W Estep
- Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - George M Church
- Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Radoje Drmanac
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Brock A Peters
- Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA. .,BGI-Shenzhen, Shenzhen, 518083, China.
| |
Collapse
|
214
|
A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nat Commun 2016; 7:12989. [PMID: 27708267 PMCID: PMC5059695 DOI: 10.1038/ncomms12989] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023] Open
Abstract
Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.
Collapse
|
215
|
Ge X, Gong H, Dumas K, Litwin J, Phillips JJ, Waisfisz Q, Weiss MM, Hendriks Y, Stuurman KE, Nelson SF, Grody WW, Lee H, Kwok PY, Shieh JT. Missense-depleted regions in population exomes implicate ras superfamily nucleotide-binding protein alteration in patients with brain malformation. NPJ Genom Med 2016; 1. [PMID: 28868155 PMCID: PMC5576364 DOI: 10.1038/npjgenmed.2016.36] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genomic sequence interpretation can miss clinically relevant missense variants for several reasons. Rare missense variants are numerous in the exome and difficult to prioritise. Affected genes may also not have existing disease association. To improve variant prioritisation, we leverage population exome data to identify intragenic missense-depleted regions (MDRs) genome-wide that may be important in disease. We then use missense depletion analyses to help prioritise undiagnosed disease exome variants. We demonstrate application of this strategy to identify a novel gene association for human brain malformation. We identified de novo missense variants that affect the GDP/GTP-binding site of ARF1 in three unrelated patients. Corresponding functional analysis suggests ARF1 GDP/GTP-activation is affected by the specific missense mutations associated with heterotopia. These findings expand the genetic pathway underpinning neurologic disease that classically includes FLNA. ARF1 along with ARFGEF2 add further evidence implicating ARF/GEFs in the brain. Using functional ontology, top MDR-containing genes were highly enriched for nucleotide-binding function, suggesting these may be candidates for human disease. Routine consideration of MDR in the interpretation of exome data for rare diseases may help identify strong genetic factors for many severe conditions, infertility/reduction in reproductive capability, and embryonic conditions contributing to preterm loss.
Collapse
Affiliation(s)
- Xiaoyan Ge
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Henry Gong
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Dumas
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Litwin
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurologic Surgery, University of California San Francisco, San Francisco, CA, USA.,Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Quinten Waisfisz
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Yvonne Hendriks
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Kyra E Stuurman
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Stanley F Nelson
- Departments of Pathology and Laboratory Medicine, Pediatrics, and Human Genetics, Divisions of Medical Genetics and Molecular Diagnostics, University of California Los Angeles, Los Angeles, CA, USA
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine and Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Tc Shieh
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
216
|
Abstract
We report on the sequencing of 10,545 human genomes at 30×-40× coverage with an emphasis on quality metrics and novel variant and sequence discovery. We find that 84% of an individual human genome can be sequenced confidently. This high-confidence region includes 91.5% of exon sequence and 95.2% of known pathogenic variant positions. We present the distribution of over 150 million single-nucleotide variants in the coding and noncoding genome. Each newly sequenced genome contributes an average of 8,579 novel variants. In addition, each genome carries on average 0.7 Mb of sequence that is not found in the main build of the hg38 reference genome. The density of this catalog of variation allowed us to construct high-resolution profiles that define genomic sites that are highly intolerant of genetic variation. These results indicate that the data generated by deep genome sequencing is of the quality necessary for clinical use.
Collapse
|
217
|
Smith TCA, Carr AM, Eyre-Walker AC. Are sites with multiple single nucleotide variants in cancer genomes a consequence of drivers, hypermutable sites or sequencing errors? PeerJ 2016; 4:e2391. [PMID: 27688957 PMCID: PMC5036107 DOI: 10.7717/peerj.2391] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 08/01/2016] [Indexed: 11/26/2022] Open
Abstract
Across independent cancer genomes it has been observed that some sites have been recurrently hit by single nucleotide variants (SNVs). Such recurrently hit sites might be either (i) drivers of cancer that are postively selected during oncogenesis, (ii) due to mutation rate variation, or (iii) due to sequencing and assembly errors. We have investigated the cause of recurrently hit sites in a dataset of >3 million SNVs from 507 complete cancer genome sequences. We find evidence that many sites have been hit significantly more often than one would expect by chance, even taking into account the effect of the adjacent nucleotides on the rate of mutation. We find that the density of these recurrently hit sites is higher in non-coding than coding DNA and hence conclude that most of them are unlikely to be drivers. We also find that most of them are found in parts of the genome that are not uniquely mappable and hence are likely to be due to mapping errors. In support of the error hypothesis, we find that recurently hit sites are not randomly distributed across sequences from different laboratories. We fit a model to the data in which the rate of mutation is constant across sites but the rate of error varies. This model suggests that ∼4% of all SNVs are errors in this dataset, but that the rate of error varies by thousands-of-fold between sites.
Collapse
Affiliation(s)
- Thomas C A Smith
- School of Life Sciences, University of Sussex , Brighton , East Sussex , United Kingdom
| | - Antony M Carr
- Genome Damage and Stability Centre, University of Sussex , Brighton , East Sussex , United Kingdom
| | - Adam C Eyre-Walker
- School of Life Sciences, University of Sussex , Brighton , East Sussex , United Kingdom
| |
Collapse
|
218
|
Abstract
It has been long understood that mutation distribution is not completely random across genomic space and in time. Indeed, recent surprising discoveries identified multiple simultaneous mutations occurring in tiny regions within chromosomes while the rest of the genome remains relatively mutation-free. Mechanistic elucidation of these phenomena, called mutation showers, mutation clusters, or kataegis, in parallel with findings of abundant clustered mutagenesis in cancer genomes, is ongoing. So far, the combination of factors most important for clustered mutagenesis is the induction of DNA lesions within unusually long and persistent single-strand DNA intermediates. In addition to being a fascinating phenomenon, clustered mutagenesis also became an indispensable tool for identifying a previously unrecognized major source of mutation in cancer, APOBEC cytidine deaminases. Future research on clustered mutagenesis may shed light onto important mechanistic details of genome maintenance, with potentially profound implications for human health.
Collapse
Affiliation(s)
- Kin Chan
- Mechanisms of Genome Dynamics Group, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Durham, North Carolina 27709; ,
| | - Dmitry A Gordenin
- Mechanisms of Genome Dynamics Group, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Durham, North Carolina 27709; ,
| |
Collapse
|
219
|
Webster TH, Wilson Sayres MA. Genomic signatures of sex-biased demography: progress and prospects. Curr Opin Genet Dev 2016; 41:62-71. [PMID: 27599147 DOI: 10.1016/j.gde.2016.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/06/2016] [Accepted: 08/02/2016] [Indexed: 01/09/2023]
Abstract
Sex-biased demographic events have played a crucial role in shaping human history. Many of these processes affect genetic variation and can therefore leave detectable signatures in the genome because autosomal, X-linked, Y-linked, and mitochondrial DNA inheritance differ between sexes. Here, we discuss how sex-biased processes shape patterns of genetic diversity across the genome, review recent genomic evidence for sex-biased demography in modern human populations, and suggest directions for future research.
Collapse
Affiliation(s)
- Timothy H Webster
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Center for Evolution and Medicine, The Biodesign Institute at Arizona State University, Tempe, AZ 85287, USA.
| |
Collapse
|
220
|
Yamada M, De Chiara L, Seandel M. Spermatogonial Stem Cells: Implications for Genetic Disorders and Prevention. Stem Cells Dev 2016; 25:1483-1494. [PMID: 27596369 PMCID: PMC5035912 DOI: 10.1089/scd.2016.0210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Spermatogonial stem cells (SSCs) propagate mammalian spermatogenesis throughout male reproductive life by continuously self-renewing and differentiating, ultimately, into sperm. SSCs can be cultured for long periods and restore spermatogenesis upon transplantation back into the native microenvironment in vivo. Conventionally, SSC research has been focused mainly on male infertility and, to a lesser extent, on cell reprogramming. With the advent of genome-wide sequencing technology, however, human studies have uncovered a wide range of pathogenic alleles that arise in the male germ line. A subset of de novo point mutations was shown to originate in SSCs and cause congenital disorders in children. This review describes both monogenic diseases (eg, Apert syndrome) and complex disorders that are either known or suspected to be driven by mutations in SSCs. We propose that SSC culture is a suitable model for studying the origin and mechanisms of these diseases. Lastly, we discuss strategies for future clinical implementation of SSC-based technology, from detecting mutation burden by sperm screening to gene correction in vitro.
Collapse
Affiliation(s)
- Makiko Yamada
- Joan and Sanford I Weill Medical College of Cornell University, 12295, Surgery, New York, New York, United States ;
| | - Letizia De Chiara
- Joan and Sanford I Weill Medical College of Cornell University, 12295, Surgery, New York, New York, United States ;
| | - Marco Seandel
- Joan and Sanford I Weill Medical College of Cornell University, 12295, Surgery, New York, New York, United States ;
| |
Collapse
|
221
|
Scally A. The mutation rate in human evolution and demographic inference. Curr Opin Genet Dev 2016; 41:36-43. [PMID: 27589081 DOI: 10.1016/j.gde.2016.07.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023]
Abstract
The germline mutation rate has long been a major source of uncertainty in human evolutionary and demographic analyses based on genetic data, but estimates have improved substantially in recent years. I discuss our current knowledge of the mutation rate in humans and the underlying biological factors affecting it, which include generation time, parental age and other developmental and reproductive timescales. There is good evidence for a slowdown in mean mutation rate during great ape evolution, but not for a more recent change within the timescale of human genetic diversity. Hence, pending evidence to the contrary, it is reasonable to use a present-day rate of approximately 0.5×10-9bp-1year-1 in all human or hominin demographic analyses.
Collapse
Affiliation(s)
- Aylwyn Scally
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, United Kingdom.
| |
Collapse
|
222
|
Hu H, Coon H, Li M, Yandell M, Huff CD. VARPRISM: incorporating variant prioritization in tests of de novo mutation association. Genome Med 2016; 8:91. [PMID: 27562213 PMCID: PMC4997702 DOI: 10.1186/s13073-016-0341-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 08/02/2016] [Indexed: 12/18/2022] Open
Abstract
Background Patients with certain genetic diseases, such as autism spectrum disorder, have increased rates of de novo mutations within some protein-coding genes. Results We introduce the VARiant PRIoritization SuM (VARPRISM), a software package which incorporates functional variant prioritization information to improve the power to detect de novo mutations influencing disease risk. VARPRISM evaluates the consequence of any given exonic mutation on the protein sequence to estimate the likelihood that the mutation is benign or damaging and conducts a likelihood ratio test on the gene level. We analyzed the Simons Simplex Collection of 2508 parent-offspring autism trios using VARPRISM, replicating 44 genes previously implicated in autism susceptibility and identifying 20 additional candidate genes, including MYO1E, KCND3, PDCD1, DLX3, and TSPAN4 (false discovery rate < 0.3). Conclusion By incorporating functional predictions, VARPRISM improved the statistical power to identify de novo mutations increasing disease risks. VARPRISM is available at http://www.hufflab.org/software/VARPRISM. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0341-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hao Hu
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Hilary Coon
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Man Li
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Mark Yandell
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
223
|
Podolskiy DI, Lobanov AV, Kryukov GV, Gladyshev VN. Analysis of cancer genomes reveals basic features of human aging and its role in cancer development. Nat Commun 2016; 7:12157. [PMID: 27515585 PMCID: PMC4990632 DOI: 10.1038/ncomms12157] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/07/2016] [Indexed: 02/07/2023] Open
Abstract
Somatic mutations have long been implicated in aging and disease, but their impact on fitness and function is difficult to assess. Here by analysing human cancer genomes we identify mutational patterns associated with aging. Our analyses suggest that age-associated mutation load and burden double approximately every 8 years, similar to the all-cause mortality doubling time. This analysis further reveals variance in the rate of aging among different human tissues, for example, slightly accelerated aging of the reproductive system. Age-adjusted mutation load and burden correlate with the corresponding cancer incidence and precede it on average by 15 years, pointing to pre-clinical cancer development times. Behaviour of mutation load also exhibits gender differences and late-life reversals, explaining some gender-specific and late-life patterns in cancer incidence rates. Overall, this study characterizes some features of human aging and offers a mechanism for age being a risk factor for the onset of cancer. Somatic mutations are associated with disease, including cancer. Here, the authors analyse cancer genomic data and show that somatic mutations increase with age and that cancer incidence lags 15 years behind this increase, later in life, mutation and cancer incidence are reduced.
Collapse
Affiliation(s)
- Dmitriy I Podolskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alexei V Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute, Cambridge, Massachusetts 02142, USA
| |
Collapse
|
224
|
Phung TN, Huber CD, Lohmueller KE. Determining the Effect of Natural Selection on Linked Neutral Divergence across Species. PLoS Genet 2016; 12:e1006199. [PMID: 27508305 PMCID: PMC4980041 DOI: 10.1371/journal.pgen.1006199] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 06/25/2016] [Indexed: 11/18/2022] Open
Abstract
A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only if more of the genome is under purifying selection than currently believed. Our work has implications for understanding the evolution of genomes and interpreting patterns of genetic variation. Genetic variation at neutral sites can be reduced through linkage to nearby selected sites. This pattern has been used to show the widespread effects of natural selection at shaping patterns of genetic diversity across genomes from a variety of species. However, it is not entirely clear whether natural selection has an effect on neutral divergence between species. Here we show that putatively neutral divergence between closely related species (human and chimp) and between distantly related pairs of species (humans and mice) show signatures consistent with having been affected by linkage to selected sites. Further, our theoretical models and simulations show that natural selection indirectly affecting linked neutral sites can generate these patterns. Unless substantially more of the genome is under the direct effects of purifying selection than currently believed, our results argue that natural selection has played an important role in shaping variation in levels of putatively neutral sequence divergence across the genome. Our findings further suggest that divergence-based estimates of neutral mutation rate variation across the genome as well as certain estimators of population history may be confounded by linkage to selected sites.
Collapse
Affiliation(s)
- Tanya N. Phung
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Christian D. Huber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Kirk E. Lohmueller
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| |
Collapse
|
225
|
Yuen RKC, Merico D, Cao H, Pellecchia G, Alipanahi B, Thiruvahindrapuram B, Tong X, Sun Y, Cao D, Zhang T, Wu X, Jin X, Zhou Z, Liu X, Nalpathamkalam T, Walker S, Howe JL, Wang Z, MacDonald JR, Chan A, D'Abate L, Deneault E, Siu MT, Tammimies K, Uddin M, Zarrei M, Wang M, Li Y, Wang J, Wang J, Yang H, Bookman M, Bingham J, Gross SS, Loy D, Pletcher M, Marshall CR, Anagnostou E, Zwaigenbaum L, Weksberg R, Fernandez BA, Roberts W, Szatmari P, Glazer D, Frey BJ, Ring RH, Xu X, Scherer SW. Genome-wide characteristics of de novo mutations in autism. NPJ Genom Med 2016; 1:160271-1602710. [PMID: 27525107 PMCID: PMC4980121 DOI: 10.1038/npjgenmed.2016.27] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
De novo mutations (DNMs) are important in Autism Spectrum Disorder (ASD), but so far analyses have mainly been on the ~1.5% of the genome encoding genes. Here, we performed whole genome sequencing (WGS) of 200 ASD parent-child trios and characterized germline and somatic DNMs. We confirmed that the majority of germline DNMs (75.6%) originated from the father, and these increased significantly with paternal age only (p=4.2×10-10). However, when clustered DNMs (those within 20kb) were found in ASD, not only did they mostly originate from the mother (p=7.7×10-13), but they could also be found adjacent to de novo copy number variations (CNVs) where the mutation rate was significantly elevated (p=2.4×10-24). By comparing DNMs detected in controls, we found a significant enrichment of predicted damaging DNMs in ASD cases (p=8.0×10-9; OR=1.84), of which 15.6% (p=4.3×10-3) and 22.5% (p=7.0×10-5) were in the non-coding or genic non-coding, respectively. The non-coding elements most enriched for DNM were untranslated regions of genes, boundaries involved in exon-skipping and DNase I hypersensitive regions. Using microarrays and a novel outlier detection test, we also found aberrant methylation profiles in 2/185 (1.1%) of ASD cases. These same individuals carried independently identified DNMs in the ASD risk- and epigenetic- genes DNMT3A and ADNP. Our data begins to characterize different genome-wide DNMs, and highlight the contribution of non-coding variants, to the etiology of ASD.
Collapse
Affiliation(s)
- Ryan K C Yuen
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Giovanna Pellecchia
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Babak Alipanahi
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xin Tong
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Yuhui Sun
- BGI-Shenzhen, Yantian, Shenzhen, China
| | | | - Tao Zhang
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Xueli Wu
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Xin Jin
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Ze Zhou
- BGI-Shenzhen, Yantian, Shenzhen, China
| | | | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Susan Walker
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Zhuozhi Wang
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ada Chan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lia D'Abate
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Eric Deneault
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle T Siu
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Pediatric Neuropsychiatry Unit, Karolinska Institutet, Stockholm, Sweden
| | - Mohammed Uddin
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Jun Wang
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Jian Wang
- BGI-Shenzhen, Yantian, Shenzhen, China
| | | | | | | | | | - Dion Loy
- Google, Mountain View, California, USA
| | | | - Christian R Marshall
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Evdokia Anagnostou
- Bloorview Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bridget A Fernandez
- Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada; Provincial Medical Genetic Program, Eastern Health, St. John's, Newfoundland, Canada
| | - Wendy Roberts
- Autism Research Unit, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Szatmari
- Autism Research Unit, The Hospital for Sick Children, Toronto, Ontario, Canada; Child Youth and Family Services, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - David Glazer
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brendan J Frey
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | | | - Xun Xu
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
226
|
Smeds L, Qvarnström A, Ellegren H. Direct estimate of the rate of germline mutation in a bird. Genome Res 2016; 26:1211-8. [PMID: 27412854 PMCID: PMC5052036 DOI: 10.1101/gr.204669.116] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 07/12/2016] [Indexed: 12/30/2022]
Abstract
The fidelity of DNA replication together with repair mechanisms ensure that the genetic material is properly copied from one generation to another. However, on extremely rare occasions when damages to DNA or replication errors are not repaired, germline mutations can be transmitted to the next generation. Because of the rarity of these events, studying the rate at which new mutations arise across organisms has been a great challenge, especially in multicellular nonmodel organisms with large genomes. We sequenced the genomes of 11 birds from a three-generation pedigree of the collared flycatcher (Ficedula albicollis) and used highly stringent bioinformatic criteria for mutation detection and used several procedures to validate mutations, including following the stable inheritance of new mutations to subsequent generations. We identified 55 de novo mutations with a 10-fold enrichment of mutations at CpG sites and with only a modest male mutation bias. The estimated rate of mutation per site per generation was 4.6 × 10(-9), which corresponds to 2.3 × 10(-9) mutations per site per year. Compared to mammals, this is similar to mouse but about half of that reported for humans, which may be due to the higher frequency of male mutations in humans. We confirm that mutation rate scales positively with genome size and that there is a strong negative relationship between mutation rate and effective population size, in line with the drift-barrier hypothesis. Our study illustrates that it should be feasible to obtain direct estimates of the rate of mutation in essentially any organism from which family material can be obtained.
Collapse
Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| |
Collapse
|
227
|
Lenz TL, Spirin V, Jordan DM, Sunyaev SR. Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection. Mol Biol Evol 2016; 33:2555-64. [PMID: 27436009 PMCID: PMC5026253 DOI: 10.1093/molbev/msw127] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Deleterious mutations are expected to evolve under negative selection and are usually purged from the population. However, deleterious alleles segregate in the human population and some disease-associated variants are maintained at considerable frequencies. Here, we test the hypothesis that balancing selection may counteract purifying selection in neighboring regions and thus maintain deleterious variants at higher frequency than expected from their detrimental fitness effect. We first show in realistic simulations that balancing selection reduces the density of polymorphic sites surrounding a locus under balancing selection, but at the same time markedly increases the population frequency of the remaining variants, including even substantially deleterious alleles. To test the predictions of our simulations empirically, we then use whole-exome sequencing data from 6,500 human individuals and focus on the most established example for balancing selection in the human genome, the major histocompatibility complex (MHC). Our analysis shows an elevated frequency of putatively deleterious coding variants in nonhuman leukocyte antigen (non-HLA) genes localized in the MHC region. The mean frequency of these variants declined with physical distance from the classical HLA genes, indicating dependency on genetic linkage. These results reveal an indirect cost of the genetic diversity maintained by balancing selection, which has hitherto been perceived as mostly advantageous, and have implications both for the evolution of recombination and also for the epidemiology of various MHC-associated diseases.
Collapse
Affiliation(s)
- Tobias L Lenz
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Evolutionary Immunogenomics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Victor Spirin
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School
| | - Daniel M Jordan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School
| | - Shamil R Sunyaev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Program in Medical and Population Genetics, The Broad Institute, Cambridge, MA
| |
Collapse
|
228
|
Parent-of-origin-specific signatures of de novo mutations. Nat Genet 2016; 48:935-9. [PMID: 27322544 DOI: 10.1038/ng.3597] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/26/2016] [Indexed: 12/17/2022]
Abstract
De novo mutations (DNMs) originating in gametogenesis are an important source of genetic variation. We use a data set of 7,216 autosomal DNMs with resolved parent of origin from whole-genome sequencing of 816 parent-offspring trios to investigate differences between maternally and paternally derived DNMs and study the underlying mutational mechanisms. Our results show that the number of DNMs in offspring increases not only with paternal age, but also with maternal age, and that some genome regions show enrichment for maternally derived DNMs. We identify parent-of-origin-specific mutation signatures that become more pronounced with increased parental age, pointing to different mutational mechanisms in spermatogenesis and oogenesis. Moreover, we find DNMs that are spatially clustered to have a unique mutational signature with no significant differences between parental alleles, suggesting a different mutational mechanism. Our findings provide insights into the molecular mechanisms that underlie mutagenesis and are relevant to disease and evolution in humans.
Collapse
|
229
|
Hauer AJ, van Beijnum J, Vandertop WP, van den Berg R, Brouwer PA, Kappelle LJ, Ruigrok YM, Klijn CJ. Parental age and the occurrence of sporadic brain arteriovenous malformations. Int J Stroke 2016; 11:NP89-NP90. [PMID: 27312680 DOI: 10.1177/1747493016654339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Allard J Hauer
- Department of Neurology and Neurosurgery, UMC Utrecht Stroke Center, Rudolf Magnus Institute of Neurosciences, University Medical Center Utrecht, the Netherlands
| | | | - W Peter Vandertop
- Department of Neurosurgery, Neurosurgical Center Amsterdam, VU University Medical Center and Amsterdam Medical Center, Amsterdam, the Netherlands
| | - René van den Berg
- Department of Radiology, Amsterdam Medical Center, Amsterdam, the Netherlands
| | - Patrick A Brouwer
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - L Jaap Kappelle
- Department of Neurology and Neurosurgery, UMC Utrecht Stroke Center, Rudolf Magnus Institute of Neurosciences, University Medical Center Utrecht, the Netherlands
| | - Ynte M Ruigrok
- Department of Neurology and Neurosurgery, UMC Utrecht Stroke Center, Rudolf Magnus Institute of Neurosciences, University Medical Center Utrecht, the Netherlands
| | - Catharina Jm Klijn
- Department of Neurology and Neurosurgery, UMC Utrecht Stroke Center, Rudolf Magnus Institute of Neurosciences, University Medical Center Utrecht, the Netherlands.,Department of Neurology, Center for Neuroscience, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| |
Collapse
|
230
|
A loss-of-function variant in OSBPL1A predisposes to low plasma HDL cholesterol levels and impaired cholesterol efflux capacity. Atherosclerosis 2016; 249:140-7. [DOI: 10.1016/j.atherosclerosis.2016.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/02/2016] [Accepted: 04/05/2016] [Indexed: 12/25/2022]
|
231
|
Kim J, Mouw KW, Polak P, Braunstein LZ, Kamburov A, Kwiatkowski DJ, Rosenberg JE, Van Allen EM, D'Andrea A, Getz G. Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors. Nat Genet 2016; 48:600-606. [PMID: 27111033 PMCID: PMC4936490 DOI: 10.1038/ng.3557] [Citation(s) in RCA: 277] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 04/01/2016] [Indexed: 12/17/2022]
Abstract
Alterations in DNA repair pathways are common in tumors and can result in characteristic mutational signatures; however, a specific mutational signature associated with somatic alterations in the nucleotide- excision repair (NER) pathway has not yet been identified. Here we examine the mutational processes operating in urothelial cancer, a tumor type in which the core NER gene ERCC2 is significantly mutated. Analysis of three independent urothelial tumor cohorts demonstrates a strong association between somatic ERCC2 mutations and the activity of a mutational signature characterized by a broad spectrum of base changes. In addition, we note an association between the activity of this signature and smoking that is independent of ERCC2 mutation status, providing genomic evidence of tobacco-related mutagenesis in urothelial cancer. Together, these analyses identify an NER-related mutational signature and highlight the related roles of DNA damage and subsequent DNA repair in shaping tumor mutational landscape.
Collapse
Affiliation(s)
- Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Brigham & Women's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Paz Polak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Lior Z Braunstein
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Atanas Kamburov
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - David J Kwiatkowski
- Harvard Medical School, Boston, MA, USA
- Division of Pulmonary Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Jonathan E Rosenberg
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eliezer M Van Allen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alan D'Andrea
- Department of Radiation Oncology, Brigham & Women's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| |
Collapse
|
232
|
Strategies to enable the adoption of animal biotechnology to sustainably improve global food safety and security. Transgenic Res 2016; 25:575-95. [PMID: 27246007 DOI: 10.1007/s11248-016-9965-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/21/2016] [Indexed: 10/21/2022]
Abstract
The ability to generate transgenic animals has existed for over 30 years, and from those early days many predicted that the technology would have beneficial applications in agriculture. Numerous transgenic agricultural animals now exist, however to date only one product from a transgenic animal has been approved for the food chain, due in part to cumbersome regulations. Recently, new techniques such as precision breeding have emerged, which enables the introduction of desired traits without the use of transgenes. The rapidly growing human population, environmental degradation, and concerns related to zoonotic and pandemic diseases have increased pressure on the animal agriculture sector to provide a safe, secure and sustainable food supply. There is a clear need to adopt transgenic technologies as well as new methods such as gene editing and precision breeding to meet these challenges and the rising demand for animal products. To achieve this goal, cooperation, education, and communication between multiple stakeholders-including scientists, industry, farmers, governments, trade organizations, NGOs and the public-is necessary. This report is the culmination of concepts first discussed at an OECD sponsored conference and aims to identify the main barriers to the adoption of animal biotechnology, tactics for navigating those barriers, strategies to improve public perception and trust, as well as industry engagement, and actions for governments and trade organizations including the OECD to harmonize regulations and trade agreements. Specifically, the report focuses on animal biotechnologies that are intended to improve breeding and genetics and currently are not routinely used in commercial animal agriculture. We put forward recommendations on how scientists, regulators, and trade organizations can work together to ensure that the potential benefits of animal biotechnology can be realized to meet the future needs of agriculture to feed the world.
Collapse
|
233
|
Abstract
Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein-coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce deleterious amino acid substitutions. We investigate this enigma using an evolutionarily basal group of Metazoa, the stony corals (order Scleractinia, class Anthozoa, phylum Cnidaria). We show that patterns of coral gbM are similar to other invertebrate species, predicting wide and active transcription and slower sequence evolution. We also find a strong correlation between gbM and codon bias, resulting from systematic replacement of CpG bearing codons. We conclude that gbM has strong effects on codon evolution and speculate that this may influence establishment of optimal codons.
Collapse
Affiliation(s)
- Groves B Dixon
- Institute for Cell and Molecular Biology, University of Texas
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, QLD, Australia ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | | |
Collapse
|
234
|
Willems T, Gymrek M, Poznik G, Tyler-Smith C, Erlich Y, Erlich Y. Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates. Am J Hum Genet 2016; 98:919-933. [PMID: 27126583 DOI: 10.1016/j.ajhg.2016.04.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/01/2016] [Indexed: 01/23/2023] Open
Abstract
Short tandem repeats (STRs) are mutation-prone loci that span nearly 1% of the human genome. Previous studies have estimated the mutation rates of highly polymorphic STRs by using capillary electrophoresis and pedigree-based designs. Although this work has provided insights into the mutational dynamics of highly mutable STRs, the mutation rates of most others remain unknown. Here, we harnessed whole-genome sequencing data to estimate the mutation rates of Y chromosome STRs (Y-STRs) with 2-6 bp repeat units that are accessible to Illumina sequencing. We genotyped 4,500 Y-STRs by using data from the 1000 Genomes Project and the Simons Genome Diversity Project. Next, we developed MUTEA, an algorithm that infers STR mutation rates from population-scale data by using a high-resolution SNP-based phylogeny. After extensive intrinsic and extrinsic validations, we harnessed MUTEA to derive mutation-rate estimates for 702 polymorphic STRs by tracing each locus over 222,000 meioses, resulting in the largest collection of Y-STR mutation rates to date. Using our estimates, we identified determinants of STR mutation rates and built a model to predict rates for STRs across the genome. These predictions indicate that the load of de novo STR mutations is at least 75 mutations per generation, rivaling the load of all other known variant types. Finally, we identified Y-STRs with potential applications in forensics and genetic genealogy, assessed the ability to differentiate between the Y chromosomes of father-son pairs, and imputed Y-STR genotypes.
Collapse
Affiliation(s)
| | | | | | | | | | - Yaniv Erlich
- New York Genome Center, New York, NY 10013, USA; Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02139, USA; Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
235
|
Smith T, Ho G, Christodoulou J, Price EA, Onadim Z, Gauthier-Villars M, Dehainault C, Houdayer C, Parfait B, van Minkelen R, Lohman D, Eyre-Walker A. Extensive Variation in the Mutation Rate Between and Within Human Genes Associated with Mendelian Disease. Hum Mutat 2016; 37:488-94. [PMID: 26857394 DOI: 10.1002/humu.22967] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/25/2016] [Indexed: 01/05/2023]
Abstract
We have investigated whether the mutation rate varies between genes and sites using de novo mutations (DNMs) from three genes associated with Mendelian diseases (RB1, NF1, and MECP2). We show that the relative frequency of mutations at CpG dinucleotides relative to non-CpG sites varies between genes and relative to the genomic average. In particular we show that the rate of transition mutation at CpG sites relative to the rate of non-CpG transversion is substantially higher in our disease genes than amongst DNMs in general; the rate of CpG transition can be several hundred-fold greater than the rate of non-CpG transversion. We also show that the mutation rate varies significantly between sites of a particular mutational type, such as non-CpG transversion, within a gene. We estimate that for all categories of sites, except CpG transitions, there is at least a 30-fold difference in the mutation rate between the 10% of sites with the highest and lowest mutation rates. However, our best estimate is that the mutation rate varies by several hundred-fold variation. We suggest that the presence of hypermutable sites may be one reason certain genes are associated with disease.
Collapse
Affiliation(s)
- Thomas Smith
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Gladys Ho
- NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia
| | - John Christodoulou
- NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.,Disciplines of Paediatrics and Child Health and Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Elizabeth Ann Price
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, The Royal London Hospital, 80 Newark Street, London, United Kingdom
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, The Royal London Hospital, 80 Newark Street, London, United Kingdom
| | | | | | - Claude Houdayer
- Service de Génétique, Institut Curie, Paris, France.,INSERM U830, centre de recherche de l'Institut Curie, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Beatrice Parfait
- EA7331, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Service de Biochimie et de Génétique Moléculaire, Hôpital Cochin, AP-HP, Paris, France
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Netherlands
| | - Dietmar Lohman
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| |
Collapse
|
236
|
Callegari AJ. Does transcription-associated DNA damage limit lifespan? DNA Repair (Amst) 2016; 41:1-7. [PMID: 27010736 DOI: 10.1016/j.dnarep.2016.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 12/31/2022]
Abstract
Small mammals undergo an aging process similar to that of larger mammals, but aging occurs at a dramatically faster rate. This phenomenon is often assumed to be the result of damage caused by reactive oxygen species generated in mitochondria. An alternative explanation for the phenomenon is suggested here. The rate of RNA synthesis is dramatically elevated in small mammals and correlates quantitatively with the rate of aging among different mammalian species. The rate of RNA synthesis is reduced by caloric restriction and inhibition of TOR pathway signaling, two perturbations that increase lifespan in multiple metazoan species. From bacteria to man, the transcription of a gene has been found to increase the rate at which it is damaged, and a number of lines of evidence suggest that DNA damage is sufficient to induce multiple symptoms associated with normal aging. Thus, the correlations frequently found between the rate of RNA synthesis and the rate of aging could potentially reflect an important role for transcription-associated DNA damage in the aging process.
Collapse
Affiliation(s)
- A John Callegari
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
237
|
Disruption of POGZ Is Associated with Intellectual Disability and Autism Spectrum Disorders. Am J Hum Genet 2016; 98:541-552. [PMID: 26942287 DOI: 10.1016/j.ajhg.2016.02.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/05/2016] [Indexed: 12/24/2022] Open
Abstract
Intellectual disability (ID) and autism spectrum disorders (ASD) are genetically heterogeneous, and a significant number of genes have been associated with both conditions. A few mutations in POGZ have been reported in recent exome studies; however, these studies do not provide detailed clinical information. We collected the clinical and molecular data of 25 individuals with disruptive mutations in POGZ by diagnostic whole-exome, whole-genome, or targeted sequencing of 5,223 individuals with neurodevelopmental disorders (ID primarily) or by targeted resequencing of this locus in 12,041 individuals with ASD and/or ID. The rarity of disruptive mutations among unaffected individuals (2/49,401) highlights the significance (p = 4.19 × 10(-13); odds ratio = 35.8) and penetrance (65.9%) of this genetic subtype with respect to ASD and ID. By studying the entire cohort, we defined common phenotypic features of POGZ individuals, including variable levels of developmental delay (DD) and more severe speech and language delay in comparison to the severity of motor delay and coordination issues. We also identified significant associations with vision problems, microcephaly, hyperactivity, a tendency to obesity, and feeding difficulties. Some features might be explained by the high expression of POGZ, particularly in the cerebellum and pituitary, early in fetal brain development. We conducted parallel studies in Drosophila by inducing conditional knockdown of the POGZ ortholog row, further confirming that dosage of POGZ, specifically in neurons, is essential for normal learning in a habituation paradigm. Combined, the data underscore the pathogenicity of loss-of-function mutations in POGZ and define a POGZ-related phenotype enriched in specific features.
Collapse
|
238
|
Marian AJ. Clinical applications of molecular genetic discoveries. Transl Res 2016; 168:6-14. [PMID: 26548329 PMCID: PMC4718781 DOI: 10.1016/j.trsl.2015.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/13/2015] [Accepted: 10/17/2015] [Indexed: 01/08/2023]
Abstract
Genome-wide association studies of complex traits have mapped >15,000 common single nucleotide variants (SNVs). Likewise, applications of massively parallel nucleic acid sequencing technologies often referred to as next-generation sequencing to molecular genetic studies of complex traits have catalogued a large number of rare variants (population frequency of <0.01) in cases with complex traits. Moreover, high-throughput nucleic acid sequencing, variant burden analysis, and linkage studies are illuminating the presence of large number of SNVs in cases and families with single-gene disorders. The plethora of the genetic variants has exposed the formidable challenge of identifying the causal and pathogenic variants from the enormous number of innocuous common and rare variants that exist in the population and in an individual genome. The arduous task of identifying the causal and pathogenic variants is further compounded by the pleiotropic effects of the variants, complexity of cis and trans interactions in the genome, variability in phenotypic expression of the disease, as well as phenotypic plasticity, and the multifarious determinants of the phenotype. Population genetic studies offer the initial roadmaps and have the potential to elucidate novel pathways involved in the pathogenesis of the disease. However, the genome of an individual is unique, rendering unambiguous identification of the causal or pathogenic variant in a single individual exceedingly challenging. Yet, the focus of the practice of medicine is on the individual, as Sir William Osler elegantly expressed in his insightful quotation: "The good physician treats the disease; the great physician treats the patient who has the disease." The daunting task facing physicians, patients, and researchers alike is to apply the modern genetic discoveries to care of the individual with or at risk of the disease.
Collapse
Affiliation(s)
- Ali J Marian
- Center for Cardiovascular Genetics, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Tex; Center for Cardiovascular Genetics, Texas Heart Institute, Houston, Tex.
| |
Collapse
|
239
|
Genes with monoallelic expression contribute disproportionately to genetic diversity in humans. Nat Genet 2016; 48:231-237. [PMID: 26808112 PMCID: PMC4942303 DOI: 10.1038/ng.3493] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 12/23/2015] [Indexed: 12/20/2022]
Abstract
An unexpectedly large number of human autosomal genes are subject to monoallelic expression (MAE). Our analysis of 4,227 such genes uncovers surprisingly high genetic variation across human populations. This increased diversity is unlikely to reflect relaxed purifying selection. Remarkably, MAE genes exhibit an elevated recombination rate and an increased density of hypermutable sequence contexts. However, these factors do not fully account for the increased diversity. We find that the elevated nucleotide diversity of MAE genes is also associated with greater allelic age: variants in these genes tend to be older and are enriched in polymorphisms shared by Neanderthals and chimpanzees. Both synonymous and nonsynonymous alleles of MAE genes have elevated average population frequencies. We also observed strong enrichment of the MAE signature among genes reported to evolve under balancing selection. We propose that an important biological function of widespread MAE might be the generation of cell-to-cell heterogeneity; the increased genetic variation contributes to this heterogeneity.
Collapse
|
240
|
Haradhvala NJ, Polak P, Stojanov P, Covington KR, Shinbrot E, Hess JM, Rheinbay E, Kim J, Maruvka YE, Braunstein LZ, Kamburov A, Hanawalt PC, Wheeler DA, Koren A, Lawrence MS, Getz G. Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair. Cell 2016; 164:538-49. [PMID: 26806129 DOI: 10.1016/j.cell.2015.12.050] [Citation(s) in RCA: 271] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/21/2015] [Accepted: 12/24/2015] [Indexed: 12/20/2022]
Abstract
Mutational processes constantly shape the somatic genome, leading to immunity, aging, cancer, and other diseases. When cancer is the outcome, we are afforded a glimpse into these processes by the clonal expansion of the malignant cell. Here, we characterize a less explored layer of the mutational landscape of cancer: mutational asymmetries between the two DNA strands. Analyzing whole-genome sequences of 590 tumors from 14 different cancer types, we reveal widespread asymmetries across mutagenic processes, with transcriptional ("T-class") asymmetry dominating UV-, smoking-, and liver-cancer-associated mutations and replicative ("R-class") asymmetry dominating POLE-, APOBEC-, and MSI-associated mutations. We report a striking phenomenon of transcription-coupled damage (TCD) on the non-transcribed DNA strand and provide evidence that APOBEC mutagenesis occurs on the lagging-strand template during DNA replication. As more genomes are sequenced, studying and classifying their asymmetries will illuminate the underlying biological mechanisms of DNA damage and repair.
Collapse
Affiliation(s)
- Nicholas J Haradhvala
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Paz Polak
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Petar Stojanov
- Carnegie Mellon University School of Computer Science, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Kyle R Covington
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Eve Shinbrot
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Julian M Hess
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Esther Rheinbay
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Jaegil Kim
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Yosef E Maruvka
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Lior Z Braunstein
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Atanas Kamburov
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Philip C Hanawalt
- Stanford University Department of Biology, 450 Serra Mall, Stanford, CA 94305, USA
| | - David A Wheeler
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Amnon Koren
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Cornell University Department of Molecular Biology and Genetics, 526 Campus Road, Ithaca, NY 14853, USA
| | - Michael S Lawrence
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
| | - Gad Getz
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.
| |
Collapse
|
241
|
Gao Z, Wyman MJ, Sella G, Przeworski M. Interpreting the Dependence of Mutation Rates on Age and Time. PLoS Biol 2016; 14:e1002355. [PMID: 26761240 PMCID: PMC4711947 DOI: 10.1371/journal.pbio.1002355] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/11/2015] [Indexed: 01/06/2023] Open
Abstract
Mutations can originate from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that arise between replication cycles and are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell divisions, providing a framework for understanding how mutation rates depend on sex, age, and cell division rate. We show that the accrual of mutations should track cell divisions not only when mutations are replicative in origin but also when they are non-replicative and repaired efficiently. One implication is that observations from diverse fields that to date have been interpreted as pointing to a replicative origin of most mutations could instead reflect the accumulation of mutations arising from endogenous reactions or exogenous mutagens. We further find that only mutations that arise from inefficiently repaired lesions will accrue according to absolute time; thus, unless life history traits co-vary, the phylogenetic “molecular clock” should not be expected to run steadily across species. Modeling how the source of mutations relates to their rate of accumulation with age, sex, and number of cell divisions helps to explain perplexing observations about germline and somatic mutations. We relate how mutations arise to how they accumulate in different sexes, with age and with cell division. This model provides a single framework within which to interpret emerging results from evolutionary biology, human genetics, and cancer genetics. We show that the accrual of mutations should track cell divisions not only when mutations originate during DNA replication but also when they arise through non-replicative mechanisms and are repaired efficiently. This realization means that previous observations of correlations between mutation and cell division rates actually provide little support to the commonly held belief that most germline and somatic mutations arise from replication errors. We further find that only mutations that arise from inefficiently repaired lesions will accrue according to absolute time; thus, without covariation in life history traits, the phylogenetic “molecular clock” should not be expected to run at constant rates across species.
Collapse
Affiliation(s)
- Ziyue Gao
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (ZG); (MP)
| | - Minyoung J. Wyman
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- * E-mail: (ZG); (MP)
| |
Collapse
|
242
|
Seplyarskiy VB, Soldatov RA, Popadin KY, Antonarakis SE, Bazykin GA, Nikolaev SI. APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication. Genome Res 2016; 26:174-82. [PMID: 26755635 PMCID: PMC4728370 DOI: 10.1101/gr.197046.115] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 12/10/2015] [Indexed: 12/31/2022]
Abstract
APOBEC3A and APOBEC3B, cytidine deaminases of the APOBEC family, are among the main factors causing mutations in human cancers. APOBEC deaminates cytosines in single-stranded DNA (ssDNA). A fraction of the APOBEC-induced mutations occur as clusters ("kataegis") in single-stranded DNA produced during repair of double-stranded breaks (DSBs). However, the properties of the remaining 87% of nonclustered APOBEC-induced mutations, the source and the genomic distribution of the ssDNA where they occur, are largely unknown. By analyzing genomic and exomic cancer databases, we show that >33% of dispersed APOBEC-induced mutations occur on the lagging strand during DNA replication, thus unraveling the major source of ssDNA targeted by APOBEC in cancer. Although methylated cytosine is generally more mutation-prone than nonmethylated cytosine, we report that methylation reduces the rate of APOBEC-induced mutations by a factor of roughly two. Finally, we show that in cancers with extensive APOBEC-induced mutagenesis, there is almost no increase in mutation rates in late replicating regions (contrary to other cancers). Because late-replicating regions are depleted in exons, this results in a 1.3-fold higher fraction of mutations residing within exons in such cancers. This study provides novel insight into the APOBEC-induced mutagenesis and describes the peculiarity of the mutational processes in cancers with the signature of APOBEC-induced mutations.
Collapse
Affiliation(s)
- Vladimir B Seplyarskiy
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991; Pirogov Russian National Research Medical University, Moscow, Russia, 117997
| | - Ruslan A Soldatov
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Konstantin Y Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland
| | - Georgii A Bazykin
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991; Pirogov Russian National Research Medical University, Moscow, Russia, 117997
| | - Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1211 Geneva, Switzerland
| |
Collapse
|
243
|
Bartram MP, Habbig S, Pahmeyer C, Höhne M, Weber LT, Thiele H, Altmüller J, Kottoor N, Wenzel A, Krueger M, Schermer B, Benzing T, Rinschen MM, Beck BB. Three-layered proteomic characterization of a novel ACTN4 mutation unravels its pathogenic potential in FSGS. Hum Mol Genet 2016; 25:1152-64. [PMID: 26740551 DOI: 10.1093/hmg/ddv638] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/31/2015] [Indexed: 01/09/2023] Open
Abstract
Genetic diseases constitute the most important cause for end-stage renal disease in children and adolescents. Mutations in the ACTN4 gene, encoding the actin-binding protein α-actinin-4, are a rare cause of autosomal dominant familial focal segmental glomerulosclerosis (FSGS). Here, we report the identification of a novel, disease-causing ACTN4 mutation (p.G195D, de novo) in a sporadic case of childhood FSGS using next generation sequencing. Proteome analysis by quantitative mass spectrometry (MS) of patient-derived urinary epithelial cells indicated that ACTN4 levels were significantly decreased when compared with healthy controls. By resolving the peptide bearing the mutated residue, we could proof that the mutant protein is less abundant when compared with the wild-type protein. Further analyses revealed that the decreased stability of p.G195D is associated with increased ubiquitylation in the vicinity of the mutation site. We next defined the ACTN4 interactome, which was predominantly composed of cytoskeletal modulators and LIM domain-containing proteins. Interestingly, this entire group of proteins, including several highly specific ACTN4 interactors, was globally decreased in the patient-derived cells. Taken together, these data suggest a mechanistic link between ACTN4 instability and proteome perturbations of the ACTN4 interactome. Our findings advance the understanding of dominant effects exerted by ACTN4 mutations in FSGS. This study illustrates the potential of genomics and complementary, high-resolution proteomics analyses to study the pathogenicity of rare gene variants.
Collapse
Affiliation(s)
- Malte P Bartram
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Sandra Habbig
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany, Department of Pediatrics
| | - Caroline Pahmeyer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | | | | | | | | | | | - Marcus Krueger
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | | |
Collapse
|
244
|
Abstract
Genome-wide association study (GWAS) technology has been a primary method for identifying the genes responsible for diseases and other traits for the past 10 years. Over 2,000 human GWAS reports now appear in the scientific journals. The technology is continuing to improve, and has recently become accessible to researchers studying a wide variety of animals, plants and model organisms. Here, we present an overview of GWAS concepts: the underlying biology, the origins of the method, and the primary components of a GWAS experiment.
Collapse
Affiliation(s)
- Andreas Scherer
- Golden Helix, Inc, a leading DNA analytics company. University of Hagen, Germany
| | | |
Collapse
|
245
|
Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. Am J Hum Genet 2015; 97:775-89. [PMID: 26581902 DOI: 10.1016/j.ajhg.2015.10.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/13/2015] [Indexed: 12/29/2022] Open
Abstract
The rate at which human genomes mutate is a central biological parameter that has many implications for our ability to understand demographic and evolutionary phenomena. We present a method for inferring mutation and gene-conversion rates by using the number of sequence differences observed in identical-by-descent (IBD) segments together with a reconstructed model of recent population-size history. This approach is robust to, and can quantify, the presence of substantial genotyping error, as validated in coalescent simulations. We applied the method to 498 trio-phased sequenced Dutch individuals and inferred a point mutation rate of 1.66 × 10(-8) per base per generation and a rate of 1.26 × 10(-9) for <20 bp indels. By quantifying how estimates varied as a function of allele frequency, we inferred the probability that a site is involved in non-crossover gene conversion as 5.99 × 10(-6). We found that recombination does not have observable mutagenic effects after gene conversion is accounted for and that local gene-conversion rates reflect recombination rates. We detected a strong enrichment of recent deleterious variation among mismatching variants found within IBD regions and observed summary statistics of local sharing of IBD segments to closely match previously proposed metrics of background selection; however, we found no significant effects of selection on our mutation-rate estimates. We detected no evidence of strong variation of mutation rates in a number of genomic annotations obtained from several recent studies. Our analysis suggests that a mutation-rate estimate higher than that reported by recent pedigree-based studies should be adopted in the context of DNA-based demographic reconstruction.
Collapse
|
246
|
Kryukov GV, Bielski CM, Samocha K, Fromer M, Seepo S, Gentry C, Neale B, Garraway LA, Sweeney CJ, Taplin ME, Van Allen EM. Genetic Effect of Chemotherapy Exposure in Children of Testicular Cancer Survivors. Clin Cancer Res 2015; 22:2183-9. [PMID: 26631610 DOI: 10.1158/1078-0432.ccr-15-2317] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/09/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Cancer survivors express anxiety that chemotherapy exposure may lead to transmissible genetic damage in posttreatment children. Preclinical models suggest that chemotherapy exposure may result in considerable genomic alterations in postexposure progeny. Epidemiologic studies have not demonstrated a significant increase in congenital abnormalities in posttreatment children of cancer survivors, but the inherited genome-wide effect of chemotherapy exposure in humans is unknown. EXPERIMENTAL DESIGN Two testicular cancer survivors cured with chemotherapy who had children pre- and postexposure without sperm banking were identified. Familial germline whole genome sequencing (WGS) was performed for these families, and analytic methods were utilized to identify de novo alterations, including mutations, recombinations, and structural rearrangements in the pre- and postexposure offspring. RESULTS No increase in de novo germline mutations in postexposure children compared with their preexposure siblings was found. Furthermore, there were no increased short insertion/deletions, recombination frequency, or structural rearrangements in these postexposure children. CONCLUSIONS In two families of male cancer survivors, there was no transmissible genomic impact of significant mutagenic exposure in postexposure children. This study may provide possible reassuring evidence for patients undergoing chemotherapy who are unable to have pretreatment sperm cryopreservation. Expanded cohorts that utilize WGS to identify environmental exposure effects on the inherited genome may inform the generalizability of these results. Clin Cancer Res; 22(9); 2183-9. ©2015 AACR.
Collapse
Affiliation(s)
- Gregory V Kryukov
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Craig M Bielski
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kaitlin Samocha
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Menachem Fromer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts. Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York. Department of Psychiatry, Mount Sinai School of Medicine, New York, New York
| | - Sara Seepo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Carleen Gentry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Benjamin Neale
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Levi A Garraway
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Eliezer M Van Allen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| |
Collapse
|
247
|
Lipson M, Loh PR, Sankararaman S, Patterson N, Berger B, Reich D. Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes. PLoS Genet 2015; 11:e1005550. [PMID: 26562831 PMCID: PMC4642934 DOI: 10.1371/journal.pgen.1005550] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 09/03/2015] [Indexed: 01/06/2023] Open
Abstract
The human mutation rate is an essential parameter for studying the evolution of our species, interpreting present-day genetic variation, and understanding the incidence of genetic disease. Nevertheless, our current estimates of the rate are uncertain. Most notably, recent approaches based on counting de novo mutations in family pedigrees have yielded significantly smaller values than classical methods based on sequence divergence. Here, we propose a new method that uses the fine-scale human recombination map to calibrate the rate of accumulation of mutations. By comparing local heterozygosity levels in diploid genomes to the genetic distance scale over which these levels change, we are able to estimate a long-term mutation rate averaged over hundreds or thousands of generations. We infer a rate of 1.61 ± 0.13 × 10-8 mutations per base per generation, which falls in between phylogenetic and pedigree-based estimates, and we suggest possible mechanisms to reconcile our estimate with previous studies. Our results support intermediate-age divergences among human populations and between humans and other great apes.
Collapse
Affiliation(s)
- Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (ML), (DR)
| | - Po-Ru Loh
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sriram Sankararaman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Nick Patterson
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Bonnie Berger
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (ML), (DR)
| |
Collapse
|
248
|
Law CY, Chang STL, Cho SY, Yau EKC, Ng GSF, Fong NC, Lam CW. Clinical whole-exome sequencing reveals a novel missense pathogenic variant of GNAO1 in a patient with infantile-onset epilepsy. Clin Chim Acta 2015; 451:292-6. [PMID: 26485252 DOI: 10.1016/j.cca.2015.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 02/08/2023]
Abstract
BACKGROUND The cause of infantile-onset epilepsy is complex and is not easily recognized clinically, particularly in paediatric patients who present with non-specific neurological signs, no radiological abnormalities and no metabolic changes. CASE We report a case of infantile-onset epilepsy in a 10-month-old Chinese girl who presented with non-specific neurological signs, no radiological abnormalities and no biochemical disturbances. She first presented at birth with twitching movements and convulsions of an unknown aetiology. Ambulatory EEG showed epileptic rhythmic activities, the presence of asynchrony and runs of sharp waves over the right parietal and central areas. Given the non-specific neurological features and negative structural and biochemical findings, we applied clinical whole-exome sequencing (WES) to determine the underlying aetiology. WES revealed a novel heterozygous missense pathogenic variant, GNAO1:NM_020988.2:c.118G>A; NP_066268.1:p.Gly40Arg. A genetic analysis of the family confirmed the variant identified is a de novo mutation. CONCLUSIONS Clinical WES can streamline genetic analysis and sort out pathogenic genes in an unbiased approach. GNAO1 is a disease-causing gene for the autosomal dominant form of early infantile epileptic encephalopathy. The novel pathogenic variant identified in this case should contribute to our understanding of the expanding spectrum of infantile-onset epilepsy.
Collapse
Affiliation(s)
- Chun-Yiu Law
- Department of Pathology, The University of Hong Kong, Hong Kong, China
| | | | - Sun Young Cho
- Department of Laboratory Medicine, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Eric Kin-Cheong Yau
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Grace Sui-Fun Ng
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Nai-Chung Fong
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Ching-Wan Lam
- Department of Pathology, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
249
|
Houge G. [Where is the boundary between diagnostics and research?]. TIDSSKRIFT FOR DEN NORSKE LEGEFORENING 2015; 135:1632. [PMID: 26442729 DOI: 10.4045/tidsskr.15.0817] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
|
250
|
|