The DOI matches its Crossref record; 48 of the 49 references it cites were found in a registry or an index; none of the 36 sources its claims cite is checked for support yet.
Mapping copy number variation by population-scale genome sequencing
Open accessAbstract
Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.
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In the paper
“Most SVs (53%) were mapped to nucleotide resolution, which facilitated analyzing their origin and functional impact.”
§ Mapping copy number variation by population scale genome sequencing > Abstract
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
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In the paper
“observed a depletion of gene disruptions amongst high frequency deletions”
- Also stated in: § Population genetic properties of deletions · plain
“we observed a depletion of high frequency alleles among deletions intersecting with protein-coding sequence compared to other deletions (P=1.1×10−11; KS test)”
§ Mapping copy number variation by population scale genome sequencing > Abstract
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In the paper
“Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications.”
§ Mapping copy number variation by population scale genome sequencing > Abstract
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
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In the paper
“constructed a map constructed a map of SV hotspots formed by common mechanisms”
§ Mapping copy number variation by population scale genome sequencing > Abstract
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In the paper
“we observed differences in the size spectra of SVs originating from distinct formation mechanisms”
§ Mapping copy number variation by population scale genome sequencing > Abstract
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“TIGRA further enabled us to validate an additional 7,359 SVs discovered with RP or RD features by identifying the SVs’ breakpoints”
§ Mapping copy number variation by population scale genome sequencing > Extent and impact of our SV discovery set
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
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In the paper
“We initially mapped the breakpoints of 7,066 deletions and 3,299 MEIs using SR and AS features.”
§ Mapping copy number variation by population scale genome sequencing > Extent and impact of our SV discovery set
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In the paper
“deletions in genomic regions accessible to short read sequencing display extensive linkage disequilibrium (LD) with SNPs.”
§ Mapping copy number variation by population scale genome sequencing > Population genetic properties of deletions
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In the paper
“Most SVs in the release set (61%) were contributed by individual methods meeting the pre-defined specificity threshold (FDR≤10%).”
§ Mapping copy number variation by population scale genome sequencing > Construction of a high-confidence SV discovery set
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“a common deletion, previously associated with body-mass index35 (BMI), that we identified with RP, RD, and SR methods”
§ Mapping copy number variation by population scale genome sequencing > Prediction of SV candidate loci and assessment of discovery methods
What the sources say
- Not checked yetcites [35] Willer, C. J. et al. Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nature Genet. 41, 25–34 (2008)
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- It may state two separate claims as one. 37
- Probably not a substantial claim. 10
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We constructed a map of unbalanced SVs (i.e., copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations.”
§ Mapping copy number variation by population scale genome sequencing > Abstract
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- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
In the paper
“The median SV size was 729 bp (mean=8 kb), approximately four times smaller than in a recent tiling CGH based study1”
§ Mapping copy number variation by population scale genome sequencing > Extent and impact of our SV discovery set
What the sources say
- Not checked yetcites [1] Conrad, D. F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704–712 (2010) source
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In the paper
“Seventeen hundred SVs affected coding sequences, resulting in full gene overlaps or exon disruptions (Table 2), many of which led to out-of-frame exons”
§ Mapping copy number variation by population scale genome sequencing > Extent and impact of our SV discovery set
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“70.8% of the deletions and 89.6% of the insertions exhibited breakpoint microhomology/homology ranging from 2-376 bp in size, with distribution modes of 2 bp (attributable to NH) and 15 bp (attributable to MEI), respectively”
§ Mapping copy number variation by population scale genome sequencing > SV formation mechanism analysis
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- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
In the paper
“NH and NAHR based mechanisms occurred across a wide size-range, whereas VNTR expansion/shrinkage, consistent with earlier findings1, led to relatively small SV sizes”
§ Mapping copy number variation by population scale genome sequencing > SV formation mechanism analysis
What the sources say
- Not checked yetcites [1] Conrad, D. F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704–712 (2010) source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our map further enabled us to examine size spectra of SV formation mechanisms and led us to identify genomic SV hotspots that are commonly dominated by a single formation mechanism.”
§ Mapping copy number variation by population scale genome sequencing > Conclusions and discussion
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In the paper
“Most of these corresponded to NAHR hotspots, although hotspots dominated by NH and VNTR also were evident.”
§ Mapping copy number variation by population scale genome sequencing > SV formation mechanism analysis
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of the remaining SVs, 60% were classified as deletions relative to ancestral sequence, whereas the ancestral state of 17% was undetermined.”
§ Mapping copy number variation by population scale genome sequencing > SV formation mechanism analysis
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we classified 15,556 SVs in our set as novel, with an enrichment of low frequency SVs and small SVs amongst the novel variants”
§ Mapping copy number variation by population scale genome sequencing > Extent and impact of our SV discovery set
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“eight callsets (three deletion, four insertion, and one tandem duplication callset) met the pre-specified specificity threshold33 (FDR≤10%), whereas the other callsets yielded lower specificity (FDRs of 13%-89%).”
§ Mapping copy number variation by population scale genome sequencing > Prediction of SV candidate loci and assessment of discovery methods
What the sources say
- Not checked yetcites [33] The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010) source
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“out of 160 nucleotide-resolution SVs identified as tandem duplications relative to the reference genome, 91.6% were classified as duplications relative to the ancestral genome, whereas the ancestral state of 8.4% remained undetermined”
§ Mapping copy number variation by population scale genome sequencing > SV formation mechanism analysis
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“common polymorphisms (minor allele frequency (MAF) >5%) were generally shared across populations, while rare alleles were frequently observed in only one population”
§ Mapping copy number variation by population scale genome sequencing > Population genetic properties of deletions
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The 156 individuals genotyped are representative of the populations from which they were sampled, so allele-frequency patterns reflect population-level properties.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“in the low-coverage data, the individual method with the greatest accuracy (FDR=3.7%) was the second most sensitive based on our gold standard (Fig. 2B), and the most sensitive when expanding the gold standard to a larger set of individuals”
§ Mapping copy number variation by population scale genome sequencing > Prediction of SV candidate loci and assessment of discovery methods
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we inferred NH as the dominating deletion mechanism, and MEI as the dominating insertion mechanism”
§ Mapping copy number variation by population scale genome sequencing > SV formation mechanism analysis
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While most SVs intersecting with genes were deletions, several validated tandem duplications and MEIs also intersected with coding sequences”
§ Mapping copy number variation by population scale genome sequencing > Extent and impact of our SV discovery set
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
None of the sources cited for this claim have been checked yet.
In the paper
“we also compared our set to a recent survey of SVs in an individual genome37 based on capillary sequencing and array-based analyses24, and observed a similar size distribution for deletions, but differences in the size distributions of other SV classes, reflecting underlying differences in SV ascertainment”
§ Mapping copy number variation by population scale genome sequencing > Extent and impact of our SV discovery set
What the sources say
- Not checked yetcites [37] Hasin-Brumshtein, Y., Lancet, D. & Olender, T. Human olfaction: from genomic variation to phenotypic diversity. Trends Genet. 25, 178–184 (2009) source
- Not checked yetcites [24] Pang, A. W. et al. Towards a comprehensive structural variation map of an individual human genome. Genome Biol. 11, R52 (2010) source
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we observed marked insertion peaks for MEIs at 300 bp, corresponding to Alu elements, and at 6 kb, corresponding to L1/LINEs”
§ Mapping copy number variation by population scale genome sequencing > SV formation mechanism analysis
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
In the paper
“The genotypes displayed 99.1% concordance with CGH array1 based genotypes (available for 1,970 of the deletions), suggesting high genotyping accuracy.”
§ Mapping copy number variation by population scale genome sequencing > Population genetic properties of deletions
What the sources say
- Not checked yetcites [1] Conrad, D. F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704–712 (2010) source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The 156 individuals genotyped are representative of the populations from which they were sampled, so allele-frequency patterns reflect population-level properties.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A significant enrichment of NAHR near recombination hotspots (P=1.3e-15) and segmental duplications (P=3.1e-17) further contributed to the clustering”
§ Mapping copy number variation by population scale genome sequencing > SV formation mechanism analysis
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the release set comprised 22,025 deletions, 501 tandem duplications, 5,371 MEIs, and 128 non-reference insertions”
§ Mapping copy number variation by population scale genome sequencing > Construction of a high-confidence SV discovery set
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Most of these occurred in regions annotated as segmental duplications, consistent with lessened evolutionary constraintin functionally redundant gene categories22.”
§ Mapping copy number variation by population scale genome sequencing > Population genetic properties of deletions
What the sources say
- Not checked yetcites [22] Kidd, J. M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56–64 (2008) source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The 156 individuals genotyped are representative of the populations from which they were sampled, so allele-frequency patterns reflect population-level properties.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“We observed several candidates for monomorphic deletions (i.e., genomic segments putatively deleted in all individuals), explainable by rare insertions present in the reference genome or by remaining genotyping inaccuracies”
§ Mapping copy number variation by population scale genome sequencing > Population genetic properties of deletions
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The 156 individuals genotyped are representative of the populations from which they were sampled, so allele-frequency patterns reflect population-level properties.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we observed notable differences between methods (Fig. 2ABC) in terms of genomic regions ascertained (Supplementary Fig. 1), accessible SV size-range (Fig. 2A), and breakpoint precision”
§ Mapping copy number variation by population scale genome sequencing > Prediction of SV candidate loci and assessment of discovery methods
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we estimated an overall sensitivity of deletion discovery of 82% in the trios, and 69% in low-coverage sequence (Fig. 2B) using a 1 bp overlap criterion.”
§ Mapping copy number variation by population scale genome sequencing > Construction of a high-confidence SV discovery set
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Altogether, we mapped ~15,000 SVs at nucleotide resolution, 48% of which were novel.”
§ Mapping copy number variation by population scale genome sequencing > Extent and impact of our SV discovery set
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“in the trios the highest sensitivities were achieved by RD and RP methods with FDR>10%”
§ Mapping copy number variation by population scale genome sequencing > Prediction of SV candidate loci and assessment of discovery methods
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“of the 11,254 nucleotide-resolution SVs discovered as deletions relative to a human reference, 21% actually represented insertion and 2% represented tandem duplications relative to the putative ancestral genome.”
§ Mapping copy number variation by population scale genome sequencing > SV formation mechanism analysis
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
In the paper
“The clustering was influenced by an abundance of VNTR near the centromeres43 and NAHR near the telomeres”
§ Mapping copy number variation by population scale genome sequencing > SV formation mechanism analysis
What the sources say
- Not checked yetcites [43] Lee, J. A., Carvalho, C. M. & Lupski, J. R. A. DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131, 1235–1247 (2007) source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“this alternative approach resulted in an increased number (by ~13%) of high-specificity (FDR<10%) calls compared to the release set (Supplementary Text), it overall resulted in fewer SV calls owing to its decreased sensitivity at the lower (<200bp) SV size range.”
§ Mapping copy number variation by population scale genome sequencing > Construction of a high-confidence SV discovery set
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“SVs have already been associated with diverse diseases, including autism2,3, schizophrenia4,5 and Crohn’s disease6,7.”
§ Mapping copy number variation by population scale genome sequencing > Introduction
What the sources say
- Not checked yetcites [2] Pinto, D. et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466, 368–372 (2010) source
- Not checked yetcites [3] Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445–449 (2007) source
- Not checked yetcites [4] Stefansson, H. et al. Large recurrent microdeletions associated with schizophrenia. Nature 455, 232–236 (2008) source
- Not checked yetcites [5] McCarthy, S. E. et al. Microduplications of 16p11.2 are associated with schizophrenia. Nature Genet. 41, 1223–1227 (2009) source
- Not checked yetcites [6] Craddock, N. et al. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464, 713–720 (2010) source
- Not checked yetcites [7] McCarroll, S. A. et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn’s disease. Nature Genet. 40, 1107–1112 (2008) source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“locus-specific studies suggest that diverse mechanisms may form SVs de novo, with some mechanisms involving complex rearrangements resulting in multiple chromosomal breakpoints8,9.”
§ Mapping copy number variation by population scale genome sequencing > Introduction
What the sources say
- Not checked yetcites [8] Hastings, P. J., Lupski, J. R., Rosenberg, S. M. & Ira, G. Mechanisms of change in gene copy number. Nature Rev. Genet. 10, 551–564 (2009) source
- Not checked yetcites [9] Stankiewicz, P. & Lupski, J. R. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61, 437–455 (2010) source
Strength:hedged· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“This method, Genome STRiP (to be described elsewhere36), integrated both RP and RD features (PD), implying that considering different evidence types can improve SV discovery.”
§ Mapping copy number variation by population scale genome sequencing > Prediction of SV candidate loci and assessment of discovery methods
What the sources say
- Not checked yetcites [36] Levy, S. et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007) source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“the LD properties of complex SVs (e.g., multiallelic SV) have not yet been fully ascertained as methods for genotyping such SVs with similar accuracy still being developed.”
§ Mapping copy number variation by population scale genome sequencing > Population genetic properties of deletions
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“we carried out extensive validations (Methods), including PCRs for over 3,000 candidate loci, and microarray data analyses for 50,000 candidate loci”
§ Mapping copy number variation by population scale genome sequencing > Prediction of SV candidate loci and assessment of discovery methods
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our fine-scale map enabled us to examine the functional impact of SVs, as exemplified by our analysis of gene disruption variants, which will be of value for genome and exome sequencing studies.”
§ Mapping copy number variation by population scale genome sequencing > Conclusions and discussion
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Sequence-based SV discovery approaches have thus far been applied to a limited (<20) number of genomes, leaving the fine-scale architecture of most common SVs unknown.”
§ Mapping copy number variation by population scale genome sequencing > Introduction
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Nucleotide resolution data allow the construction of reference datasets and make SVs readily assessable across different experimental platforms using genotyping approaches.”
§ Mapping copy number variation by population scale genome sequencing > Conclusions and discussion
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In the paper
“High levels of structural variation, including copy-number variation, were previously described for both processes15,22,39.”
§ Mapping copy number variation by population scale genome sequencing > Extent and impact of our SV discovery set
What the sources say
- Not checked yetcites [15] Korbel, J. O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420–426 (2007) source
- Not checked yetcites [22] Kidd, J. M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56–64 (2008) source
- Not checked yetcites [39] Altshuler, D. M. et al. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52–58 (2010) source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“a detailed SV characterization, including analyses of SV origin and impact, requires knowledge of precise SV sequences.”
§ Mapping copy number variation by population scale genome sequencing > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
In the paper
“The 1000GP recently generated 4.1 Terabases of raw sequence in pilot projects targeting whole human genomes33”
§ Mapping copy number variation by population scale genome sequencing > Introduction
What the sources say
- Not checked yetcites [33] The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010) source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Recurrent rearrangements, implicated in genomic disorders, are hypothesized to be associated with local genome architecture44, e.g., with segmental duplications that facilitate NAHR.”
§ Mapping copy number variation by population scale genome sequencing > Conclusions and discussion
What the sources say
- Not checked yetcites [44] Harrow, J. et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 7, (suppl. 1)S4 (2006) source
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“DNA rearrangement in the absence of homology, i.e., MMBIR, has been implicated in recurrent SV formation8,45.”
§ Mapping copy number variation by population scale genome sequencing > Conclusions and discussion
What the sources say
- Not checked yetcites [8] Hastings, P. J., Lupski, J. R., Rosenberg, S. M. & Ira, G. Mechanisms of change in gene copy number. Nature Rev. Genet. 10, 551–564 (2009) source
- Not checked yetcites [45]
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Our study focused on characterizing deletions, which are often associated with disease9.”
§ Mapping copy number variation by population scale genome sequencing > Conclusions and discussion
What the sources say
- Not checked yetcites [9] Stankiewicz, P. & Lupski, J. R. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61, 437–455 (2010) source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“our analysis revealed a map of SV hotspots that may constitute local centers of de novo SV formation, consistent with the concept that local genome architecture contributes to genomic instability44.”
§ Mapping copy number variation by population scale genome sequencing > Conclusions and discussion
What the sources say
- Not checked yetcites [44] Harrow, J. et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 7, (suppl. 1)S4 (2006) source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Systematic characterization of SVs in these genomes will benefit from the concepts and datasets presented here.”
§ Mapping copy number variation by population scale genome sequencing > Conclusions and discussion
Tests✓ Asserted: passes✗ Checkable: fails✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may be too vague to check against evidence.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“most SV discovery methods depend on mapping reads onto their genomic locus of origin, i.e., the ‘accessible’ fraction of the genome, a fraction lessened in segmental duplications”
§ Mapping copy number variation by population scale genome sequencing > Conclusions and discussion
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
- Rests on an assumption: The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
The paper relies on this without support.
The 156 individuals genotyped are representative of the populations from which they were sampled, so allele-frequency patterns reflect population-level properties.
“we generated genotypes for 13,826 autosomal deletions in 156 individuals”
The paper relies on this without support.
The human reference genome assembly is a valid representation of the reference sequence for identifying structural variants.
“identifying SVs as genomic differences relative to a human reference”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“On average, there are >1000 CNVs in the genome, accounting for ~4 million base pairs of genomic difference (Conrad et al., 2010; Mills et al., 2011).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Mills et al., 2011
In the citing paper
“In truth, structural variants come in many shapes, sizes and allele frequencies, and a majority of variants present in an individual genome are common alleles (Conrad et al., 2010; McCarroll et al., 2008; Mills et al., 2011; Sudmant et al., 2010).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Mills et al., 2011
In the citing paper
“Large deletions or duplications showed extensive stretches of sequence of >95% identity at breakpoints, suggesting that they were generated by NAHR.”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Mills et al., 2011
In the citing paper
“Approximately 70.8% of the deletions were attributed to either a non homology based mechanism (i.e., NHEJ) or MMBIR.”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Mills et al., 2011
In the citing paper
“Most tandem duplications displayed microhomology of 2–17 basepairs at breakpoints, indicating that they are likely formed by FoSTeS/MMBIR.”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Mills et al., 2011
In the citing paper
“89.6% of small insertions were attributable to retrotransposition activity.”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Mills et al., 2011
Citations
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Metadata
- Authors
- 1000 Genomes Project, Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., Cheetham, R. K., Chinwalla, A., Conrad, D. F., Fu, Y., Grubert, F., Hajirasouliha, I., Hormozdiari, F., Iakoucheva, L. M., Iqbal, Z., Kang, S., Kidd, J. M., Konkel, M. K., Korn, J., Khurana, E., Kural, D., Lam, H. Y. K., Leng, J., Li, R., Li, Y., Lin, C.-Y., Luo, R., Mu, X. J., Nemesh, J., Peckham, H. E., Rausch, T., Scally, A., Shi, X., Stromberg, M. P., Stütz, A. M., Urban, A. E., Walker, J. A., Wu, J., Zhang, Y., Zhang, Z. D., Batzer, M. A., Ding, L., Marth, G. T., McVean, G., Sebat, J., Snyder, M., Wang, J., Ye, K., Eichler, E. E., Gerstein, M. B., Hurles, M. E., Lee, C., McCarroll, S. A., & Korbel, J. O.
- Affiliations
- Brigham and Women's Hospital (US)
- Boston College (US)
- Broad Institute (US)
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- Yale University (US)
- Leiden University Medical Center (NL)
- Washington University in St. Louis (US)
- Wellcome Sanger Institute (GB)
- Stanford University (US)
- Simon Fraser University (CA)
- Centre for Human Genetics (GB)
- Louisiana State University (US)
- BGI Group (China) (CN)
- European Molecular Biology Laboratory (DE)
- University of California San Diego (US)
- Corresponding author
- Korbel, Jan O.
- ORCID
- Mills, Ryan E.
- Walter, Klaudia
- Stewart, Chip
- Handsaker, Robert E.
- Chen, Ken
- Alkan, Can
- Abyzov, Alexej
- Ye, Kai
- Chinwalla, Asif
- Conrad, Donald F.
- Hajirasouliha, Iman
- Hormozdiari, Fereydoun
- Iakoucheva, Lilia M.
- Iqbal, Zamin
- Kidd, Jeffrey M.
- Konkel, Miriam K.
- Korn, Joshua
- Khurana, Ekta
- Kural, Deniz
- Lam, Hugo Y. K.
- Leng, Jing
- Li, Ruiqiang
- Li, Yingrui
- Lin, Chang-Yun
- Luo, Ruibang
- Mu, Xinmeng Jasmine
- Rausch, Tobias
- Scally, Aylwyn
- Shi, Xinghua
- Stütz, Adrian M.
- Urban, Alexander Eckehart
- Zhang, Zhengdong D.
- Batzer, Mark A.
- Ding, Li
- McVean, Gil
- Sebat, Jonathan
- Snyder, Michael
- Wang, Jun
- Ye, Kenny
- Eichler, Evan E.
- Gerstein, Mark B.
- Hurles, Matthew E.
- Lee, Charles
- McCarroll, Steven A.
- Korbel, Jan O.
- Venue
- Nature
- Published
- 2011-02
- Volume
- 470
- Issue
- 7332
- Pages
- 59-65
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3077050
- OpenAlex
- W2116126626
- Cited by
- 1,140
- References
- 49
- Citations by year
- 2026: 14 · 2025: 37 · 2024: 54 · 2023: 33 · 2022: 41 · 2021: 62 · 2020: 61 · 2019: 68 · 2018: 55 · 2017: 70 · 2016: 81 · 2015: 113 · 2014: 117 · 2013: 117 · 2012: 128
- FWCI
- 88.14
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Civil War Book Review (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- eScholarship (California Digital Library) (submittedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- PMC
- Funders
- Wellcome Trust (085532, 062023, 077009, 077192, 077014)
- National Institute for Health and Care Research (NF-SI-0508-10212)
- National Institutes of Health (5p41hg004221-03)
- National Institute on Alcohol Abuse and Alcoholism (R21AA022707)
- National Institute of Mental Health (R01MH091350)
- National Human Genome Research Institute (U54HG003067, U54HG003273, R01HG004719, U01HG005209, RC2HG005552, P41-HG004221)
- National Institute of General Medical Sciences (R01GM059290, R01GM081533)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- copy number variation, structural variants, deletion mapping, tandem duplication, insertion, gene deletion, human genetic variation
- MeSH terms
- Genetics, Population, Genotype, Humans, Reproducibility of Results, Genome, Human, Mutagenesis, Insertional, Sequence Deletion, Sequence Analysis, DNA, Genetic Predisposition to Disease, Gene Duplication, Genomics, DNA Copy Number Variations
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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