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Article: The difficulty of avoiding false positives in genome scans for natural selection.

Mallick, Swapan / Gnerre, Sante / Muller, Paul / Reich, David

2009 Volume 19, Issue 5, Page(s) 922–933

Abstract: Several studies have found evidence for more positive selection on the chimpanzee lineage compared with the human lineage since the two species split. A potential concern, however, is that these findings may simply reflect artifacts of the data: ... ...

Abstract	Several studies have found evidence for more positive selection on the chimpanzee lineage compared with the human lineage since the two species split. A potential concern, however, is that these findings may simply reflect artifacts of the data: inaccuracies in the underlying chimpanzee genome sequence, which is of lower quality than human. To test this hypothesis, we generated de novo genome assemblies of chimpanzee and macaque and aligned them with human. We also implemented a novel bioinformatic procedure for producing alignments of closely related species that uses synteny information to remove misassembled and misaligned regions, and sequence quality scores to remove nucleotides that are less reliable. We applied this procedure to re-examine 59 genes recently identified as candidates for positive selection in chimpanzees. The great majority of these signals disappear after application of our new bioinformatic procedure. We also carried out laboratory-based resequencing of 10 of the regions in multiple chimpanzees and humans, and found that our alignments were correct wherever there was a conflict with the published results. These findings throw into question previous findings that there has been more positive selection in chimpanzees than in humans since the two species diverged. Our study also highlights the challenges of searching the extreme tails of distributions for signals of natural selection. Inaccuracies in the genome sequence at even a tiny fraction of genes can produce false-positive signals, which make it difficult to identify loci that have genuinely been targets of selection.
MeSH term(s)	Animals ; Base Sequence ; Evolution, Molecular ; Genome ; Genomics ; Humans ; Molecular Sequence Data ; Pan troglodytes/genetics ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Synteny
Language	English
Publishing date	2009-05-01
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.086512.108
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Article ; Online: Assisted assembly: how to improve a de novo genome assembly by using related species.

Gnerre, Sante / Lander, Eric S / Lindblad-Toh, Kerstin / Jaffe, David B

Genome biology

2009 Volume 10, Issue 8, Page(s) R88

Abstract: We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an assisting process via a related genome. We show that the ... ...

Abstract	We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an assisting process via a related genome. We show that the information provided by aligning the whole-genome shotgun reads of the target against a reference genome can be used to substantially improve the quality of the resulting assembly.
MeSH term(s)	Algorithms ; Animals ; Computational Biology/methods ; Genome ; Humans ; Mammals/genetics ; Plasmodium/genetics
Language	English
Publishing date	2009-08-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/gb-2009-10-8-r88
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Article: Assisted assembly: how to improve a de novo genome assembly by using related species

Gnerre, Sante / David B Jaffe / Eric S Lander / Kerstin Lindblad-Toh

Genome biology. 2009 Aug., v. 10, no. 8

2009

Abstract	We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an assisting process via a related genome. We show that the information provided by aligning the whole-genome shotgun reads of the target against a reference genome can be used to substantially improve the quality of the resulting assembly.
Keywords	algorithms ; genome ; genome assembly
Language	English
Dates of publication	2009-08
Size	p. 2238.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2009-10-8-r88
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Article ; Online: De novo assembly of highly diverse viral populations

Yang Xiao / Charlebois Patrick / Gnerre Sante / Coole Matthew G / Lennon Niall J / Levin Joshua Z / Qu James / Ryan Elizabeth M / Zody Michael C / Henn Matthew R

BMC Genomics, Vol 13, Iss 1, p

2012 Volume 475

Abstract: Abstract Background Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is ... ...

Abstract	Abstract Background Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. Results We present VICUNA , a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software . Conclusions We developed VICUNA , a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.
Keywords	Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Language	English
Publishing date	2012-09-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genetic evidence for complex speciation of humans and chimpanzees.

Patterson, Nick / Richter, Daniel J / Gnerre, Sante / Lander, Eric S / Reich, David

Nature

2006 Volume 441, Issue 7097, Page(s) 1103–1108

Abstract: The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million ... ...

Abstract	The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human-chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our analysis also shows that human-chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.
MeSH term(s)	Animals ; Evolution, Molecular ; Genetic Speciation ; Genome ; Genomics ; Humans ; Hybridization, Genetic ; Models, Genetic ; Pan troglodytes/genetics ; Primates/genetics ; Time Factors ; X Chromosome/genetics
Language	English
Publishing date	2006-06-29
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature04789
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Article ; Online: Closing gaps in the human genome using sequencing by synthesis.

Garber, Manuel / Zody, Michael C / Arachchi, Harindra M / Berlin, Aaron / Gnerre, Sante / Green, Lisa M / Lennon, Niall / Nusbaum, Chad

Genome biology

2009 Volume 10, Issue 6, Page(s) R60

Abstract: The most recent release of the finished human genome contains 260 euchromatic gaps (excluding chromosome Y). Recent work has helped explain a large number of these unresolved regions as 'structural' in nature. Another class of gaps is likely to be ... ...

Abstract	The most recent release of the finished human genome contains 260 euchromatic gaps (excluding chromosome Y). Recent work has helped explain a large number of these unresolved regions as 'structural' in nature. Another class of gaps is likely to be refractory to clone-based approaches, and cannot be approached in ways previously described. We present an approach for closing these gaps using 454 sequencing. As a proof of principle, we closed all three remaining non-structural gaps in chromosome 15.
MeSH term(s)	Base Sequence ; Cell Line ; Chromosomes, Human, Pair 15/genetics ; Genome, Human ; Humans ; Sequence Analysis, DNA/methods
Language	English
Publishing date	2009-06-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/gb-2009-10-6-r60
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Article ; Online: Analysis of chimpanzee history based on genome sequence alignments.

Caswell, Jennifer L / Mallick, Swapan / Richter, Daniel J / Neubauer, Julie / Schirmer, Christine / Gnerre, Sante / Reich, David

PLoS genetics

2008 Volume 4, Issue 4, Page(s) e1000057

Abstract: Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence ... ...

Abstract	Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously available. We show that bonobos and common chimpanzees were separated approximately 1,290,000 years ago, western and other common chimpanzees approximately 510,000 years ago, and eastern and central chimpanzees at least 50,000 years ago. We infer that the central chimpanzee population size increased by at least a factor of 4 since its separation from western chimpanzees, while the western chimpanzee effective population size decreased. Surprisingly, in about one percent of the genome, the genetic relationships between humans, chimpanzees, and bonobos appear to be different from the species relationships. We used PCR-based resequencing to confirm 11 regions where chimpanzees and bonobos are not most closely related. Study of such loci should provide information about the period of time 5-7 million years ago when the ancestors of humans separated from those of the chimpanzees.
MeSH term(s)	Animals ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Genome ; Genome, Human ; Genomics ; Humans ; Pan paniscus/genetics ; Pan troglodytes/genetics ; Sequence Alignment
Language	English
Publishing date	2008-04-18
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1000057
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Article ; Online: De novo assembly of highly diverse viral populations.

Yang, Xiao / Charlebois, Patrick / Gnerre, Sante / Coole, Matthew G / Lennon, Niall J / Levin, Joshua Z / Qu, James / Ryan, Elizabeth M / Zody, Michael C / Henn, Matthew R

BMC genomics

2012 Volume 13, Page(s) 475

Abstract: Background: Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both ...

Abstract	Background: Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. Results: We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software. Conclusions: We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.
MeSH term(s)	Algorithms ; Computational Biology ; Genome, Viral/genetics ; Software
Language	English
Publishing date	2012-09-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/1471-2164-13-475
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Article ; Online: A direct characterization of human mutation based on microsatellites.

Sun, James X / Helgason, Agnar / Masson, Gisli / Ebenesersdóttir, Sigríður Sunna / Li, Heng / Mallick, Swapan / Gnerre, Sante / Patterson, Nick / Kong, Augustine / Reich, David / Stefansson, Kari

Nature genetics

2012 Volume 44, Issue 10, Page(s) 1161–1165

Abstract: Mutations are the raw material of evolution but have been difficult to study directly. We report the largest study of new mutations to date, comprising 2,058 germline changes discovered by analyzing 85,289 Icelanders at 2,477 microsatellites. The ... ...

Abstract	Mutations are the raw material of evolution but have been difficult to study directly. We report the largest study of new mutations to date, comprising 2,058 germline changes discovered by analyzing 85,289 Icelanders at 2,477 microsatellites. The paternal-to-maternal mutation rate ratio is 3.3, and the rate in fathers doubles from age 20 to 58, whereas there is no association with age in mothers. Longer microsatellite alleles are more mutagenic and tend to decrease in length, whereas the opposite is seen for shorter alleles. We use these empirical observations to build a model that we apply to individuals for whom we have both genome sequence and microsatellite data, allowing us to estimate key parameters of evolution without calibration to the fossil record. We infer that the sequence mutation rate is 1.4-2.3×10(-8) mutations per base pair per generation (90% credible interval) and that human-chimpanzee speciation occurred 3.7-6.6 million years ago.
MeSH term(s)	Bayes Theorem ; Evolution, Molecular ; Female ; Genetic Speciation ; Genome, Human ; Germ-Line Mutation ; Humans ; Male ; Markov Chains ; Microsatellite Repeats ; Models, Genetic ; Monte Carlo Method ; Pedigree
Language	English
Publishing date	2012-08-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/ng.2398
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Article: Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer.

Janku, Filip / Zhang, Shile / Waters, Jill / Liu, Li / Huang, Helen J / Subbiah, Vivek / Hong, David S / Karp, Daniel D / Fu, Siqing / Cai, Xuyu / Ramzanali, Nishma M / Madwani, Kiran / Cabrilo, Goran / Andrews, Debra L / Zhao, Yue / Javle, Milind / Kopetz, E Scott / Luthra, Rajyalakshmi / Kim, Hyunsung J /

Gnerre, Sante / Satya, Ravi Vijaya / Chuang, Han-Yu / Kruglyak, Kristina M / Toung, Jonathan / Zhao, Chen / Shen, Richard / Heymach, John V / Meric-Bernstam, Funda / Mills, Gordon B / Fan, Jian-Bing / Salathia, Neeraj S

Clinical cancer research : an official journal of the American Association for Cancer Research

2017 Volume 23, Issue 18, Page(s) 5648–5656

Abstract: Purpose: ...

Abstract	Purpose:
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Biomarkers, Tumor ; Circulating Tumor DNA ; Female ; Genetic Testing ; High-Throughput Nucleotide Sequencing/methods ; High-Throughput Nucleotide Sequencing/standards ; Humans ; Male ; Middle Aged ; Mutation ; Neoplasms/diagnosis ; Neoplasms/genetics ; Neoplasms/mortality ; Prognosis ; Reproducibility of Results ; Sensitivity and Specificity
Chemical Substances	Biomarkers, Tumor ; Circulating Tumor DNA
Language	English
Publishing date	2017-05-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-17-0291
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