Initial sequencing and analysis of the human genome.
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Abstract: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
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TL;DR: Large‐scale, well‐designed studies are required to clarify the actual role of this factor and other genetic variants in liver fibrosis, as some of the studies have yielded contradictory results.
341 citations
TL;DR: Two strategies for MCS identification are reported, demonstrating their ability to detect virtually all known actively conserved sequences but very little neutrally evolving sequence (specifically, ancestral repeats).
Abstract: A key component of genomics research beyond the Human Genome Project will be the rigorous interpretation of the recently finished human genome sequence (Collins et al. 2003). Central to these efforts will be the identification of all functional elements in the human genome. Recent comparative analyses of the human and mouse genome sequences suggest that ∼5% of the mammalian genome is under active selection and thus likely serves a functional role (International Mouse Genome Sequencing Consortium 2002; Roskin et al. 2003). Within this functional subset is an estimated 1% to 2% of the genome that encodes protein (International Mouse Genome Sequencing Consortium 2002). The prospects for comprehensive identification of these coding sequences are quite good, especially in light of the availability of data sets that are complementary to the genomic sequence (e.g., ESTs [Boguski et al. 1994; also see http://www.ncbi.nlm.nih.gov/dbEST] and full-length cDNA sequences [Strausberg et al. 2002; also see http://mgc.nci.nih.gov]) and ever-improving computational methods for gene prediction (Kulp et al. 1996; Burge and Karlin 1997; Rogic et al. 2001; Solovyev 2001; Flicek et al. 2003). The complete identification and characterization of the remaining 3% to 4% of the mammalian genome that likely corresponds to functional non-coding sequence will be profoundly more challenging, due to the lack of complementary data sets, the absence of robust tools for computational predictions, and the incomplete insight about the nature of such sequence. In short, the generation of a comprehensive “parts list” of functional elements in the human genome remains an immense and important challenge.
The comparison of orthologous genomic sequences has emerged as a powerful approach for identifying functional elements in the genome (Dermitzakis et al. 2002; DeSilva et al. 2002). The premise of this approach is that sequences conserved across millions of years of evolution are likely to have a functional role (Pennacchio and Rubin 2001). Comparative sequence analyses have been shown to facilitate the identification of both coding (Batzoglou et al. 2000; Korf et al. 2001; Pennacchio et al. 2001; Alexandersson et al. 2003; Flicek et al. 2003) and functional non-coding (Stojanovic et al. 1999; Dubchak et al. 2000; Gottgens et al. 2000; Loots et al. 2000, 2002; Wasserman et al. 2000; Dehal et al. 2001; Elnitski et al. 2003; Kellis et al. 2003) sequences. Among the latter are elements that regulate the spatial and temporal patterns of gene expression (Hardison 2000). When the generation of alignments between related sequences is not possible, motif-finding techniques have also been used to identify functional sequences, in particular for detecting transcription factor–binding sites (Bailey and Elkan 1995; Roth et al. 1998; Hertz and Stormo 1999; McCue et al. 2001; Blanchette and Tompa 2002).
Recent efforts have produced whole-genome sequences for several vertebrates, including human (International Human Genome Sequencing Consortium 2001), mouse (International Mouse Genome Sequencing Consortium 2002), rat (http://genome.ucsc.edu/cgi-bin/hgGateway?org=rat), and pufferfish (Aparicio et al. 2002), with the sequencing of additional vertebrate genomes well underway. Increasingly, methods for visualizing (Kent et al. 2002; Clamp et al. 2003; Karolchik et al. 2003) and comparing (Stojanovic et al. 1999; Mayor et al. 2000; Blanchette and Tompa 2002; Loots et al. 2002; Giardine et al. 2003; Schwartz et al. 2003a) genomic sequences from multiple species are emerging. As a complement to these efforts, we are generating the sequence of targeted genomic regions in multiple, phylogenetically diverse vertebrates (Thomas et al. 2003) and developing computational approaches for identifying the subset of sequences that confers function. In particular, we have focused on developing algorithms for detecting sequences that are highly conserved across multiple species, which we call Multi-species Conserved Sequences (or MCSs); such sequences represent candidates for being functionally important. Here we report the development and testing of methods for MCS detection, including analyses of MCSs identified using a recently generated set of orthologous sequences from 11 non-human vertebrates (Thomas et al. 2003).
341 citations
TL;DR: The value of high-coverage sequencing for constructing population-specific variant panels, which covers 99.0% SNVs of minor allele frequency ≥0.1%, is demonstrated, and its value for identifying causal rare variants of complex human disease phenotypes in genetic association studies is demonstrated.
Abstract: The Tohoku Medical Megabank Organization reports the whole-genome sequences of 1,070 healthy Japanese individuals and construction of a Japanese population reference panel (1KJPN). Here we identify through this high-coverage sequencing (32.4 × on average), 21.2 million, including 12 million novel, single-nucleotide variants (SNVs) at an estimated false discovery rate of <1.0%. This detailed analysis detected signatures for purifying selection on regulatory elements as well as coding regions. We also catalogue structural variants, including 3.4 million insertions and deletions, and 25,923 genic copy-number variants. The 1KJPN was effective for imputing genotypes of the Japanese population genome wide. These data demonstrate the value of high-coverage sequencing for constructing population-specific variant panels, which covers 99.0% SNVs of minor allele frequency ≥0.1%, and its value for identifying causal rare variants of complex human disease phenotypes in genetic association studies.
340 citations
TL;DR: The combined analysis of the EST database and six BAC clones leads to the prediction that the tomato genome encodes ∼35,000 genes, which are sequestered largely in euchromatic regions corresponding to less than one-quarter of the total DNA in the tomato nucleus.
Abstract: Analysis of a collection of 120,892 single-pass ESTs, derived from 26 different tomato cDNA libraries and reduced to a set of 27,274 unique consensus sequences (unigenes), revealed that 70% of the unigenes have identifiable homologs in the Arabidopsis genome. Genes corresponding to metabolism have remained most conserved between these two genomes, whereas genes encoding transcription factors are among the fastest evolving. The majority of the 10 largest conserved multigene families share similar copy numbers in tomato and Arabidopsis, suggesting that the multiplicity of these families may have occurred before the divergence of these two species. An exception to this multigene conservation was observed for the E8-like protein family, which is associated with fruit ripening and has higher copy number in tomato than in Arabidopsis. Finally, six BAC clones from different parts of the tomato genome were isolated, genetically mapped, sequenced, and annotated. The combined analysis of the EST database and these six sequenced BACs leads to the prediction that the tomato genome encodes ∼35,000 genes, which are sequestered largely in euchromatic regions corresponding to less than one-quarter of the total DNA in the tomato nucleus.
340 citations
TL;DR: The genome sequence of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals, shedding new light on the tempo and mode of gene/genome evolution in mammals and promising several research applications for the cat.
Abstract: The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing approximately 65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence.
340 citations
References
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TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
70,111 citations
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Abstract: Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).
14,075 citations
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Abstract: A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
12,098 citations
TL;DR: This letter extends the heuristic homology algorithm of Needleman & Wunsch (1970) to find a pair of segments, one from each of two long sequences, such that there is no other Pair of segments with greater similarity (homology).
10,262 citations
09 Apr 1981
TL;DR: The complete sequence of the 16,569-base pair human mitochondrial genome is presented and shows extreme economy in that the genes have none or only a few noncoding bases between them, and in many cases the termination codons are not coded in the DNA but are created post-transcriptionally by polyadenylation of the mRNAs.
Abstract: The complete sequence of the 16,569-base pair human mitochondrial genome is presented. The genes for the 12S and 16S rRNAs, 22 tRNAs, cytochrome c oxidase subunits I, II and III, ATPase subunit 6, cytochrome b and eight other predicted protein coding genes have been located. The sequence shows extreme economy in that the genes have none or only a few noncoding bases between them, and in many cases the termination codons are not coded in the DNA but are created post-transcriptionally by polyadenylation of the mRNAs.
8,783 citations