| Accession | HsInv1053 | Region of the inversion | chr7:70058904-70076823 |
| Status | Validated | Prediction type | Complex |
| Estimated Inversion Size | 15,308 bp | Supporting predictions | 10 |
| Inverted allele frequency | 0.6594 | Mechanism of origin | FoSTeS |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr7:70058904-70064121 |
| Ancestral orientation | Standard | Breakpoint 2 | chr7:70076816-70076823 |
| Comments | Derived allele includes a 5.2 kb deletion and a small duplication flanking the inverted region in breakpoint 1 (which make that some of the predictions are not completely consistent)
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
| Description | Discovery, genotyping and phasing of structural variants detected from Illumina whole genome sequencing data of 769 individuals from 250 Dutch families belonging to the GoNL project | ||||||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||||||
| Name | |||
| Breakpoint 1 | chr7:70058910-70058910 | Breakpoint 2 | chr7:70076828-70076828 |
| Individuals | |||
| Name | |||
| Breakpoint 1 | chr7:70064117-70064117 | Breakpoint 2 | chr7:70076809-70076809 |
| Individuals | |||
| Description | Integrated analysis of structural variants in 2,504 human genomes through short-read and long-read DNA sequencing and statistical imputation using the 1000 Genomes Project data | ||||||||||
| Method | Paired-end mapping (PEM), Long-read sequencing | ||||||||||
| Name | |||
| Breakpoint 1 | chr7:70058735-70058735 | Breakpoint 2 | chr7:70076888-70076888 |
| Individuals | 1596 out of 2504 individuals
 | ||
| Description | Next generation sequencing and analysis by paired-end mapping of a Korean individual genome | ||||||||||||||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr7:70058658-70058907 | Breakpoint 2 | chr7:70076553-70076824 | ||||
| Individuals |
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| Name | |||||||
| Breakpoint 1 | chr7:70064132-70064343 | Breakpoint 2 | chr7:70076854-70077069 | ||||
| Individuals |
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| Description | Next-generation sequencing and analysis by paired-end mapping of a male Han Chinese individual genome | ||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||
| Name | |||
| Breakpoint 1 | chr7:70058865-70058865 | Breakpoint 2 | chr7:70076604-70076604 |
| Individuals | |||
| Description | Sequencing and analysis of the independently assembled diploid J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Genome sequence comparison | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr7:70064121-70064121 | Breakpoint 2 | chr7:70076815-70076815 | ||||
| Individuals |
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| Description | Identification of human inversion polymorphisms by comparative analysis of human and chimpanzee genome sequence assemblies | ||||||||||
| Method | Genome sequence comparison | ||||||||||
| Name | |||
| Breakpoint 1 | chr7:70058905-70058906 | Breakpoint 2 | chr7:70076823-70076824 |
| Individuals | |||
- Martinez-Fundichely et al. 2014 (in preparation)
| Description | Accurate prediction of inversions in the human genome from Kidd et al. 2008 fosmid paired-end mapping data using the GRIAL algorithm, and validation of some predictions by sequence analysis and PCR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Name | |||||||||||||||||||||||
| Breakpoint 1 | chr7:70032007-70064629 | Breakpoint 2 | chr7:70076139-70106476 | ||||||||||||||||||||
| D/C Score | 0.75 | Disc. Support Prob. | 0.02333 | ||||||||||||||||||||
| Individuals |
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| Name | |||||||||||||||||||||||
| Breakpoint 1 | chr7:70031528-70066512 | Breakpoint 2 | chr7:70076380-70104763 | ||||||||||||||||||||
| D/C Score | 0.26 | Disc. Support Prob. | 0.71097 | ||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| Description | Validation and characterization of human inversions predicted by comparison of two independently assembled human genomes | ||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 98 individuals: 96 HapMap/1000GP, 2 Other 9 STD/STD - 41 STD/INV - 45 INV/INV - 3 ND |
| Description | Discovery, genotyping and phasing of structural variants detected from Illumina whole genome sequencing data of 769 individuals from 250 Dutch families belonging to the GoNL project | ||||||||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Comment | Tested in sample A105c |
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Comment | Tested in sample A105c |
| Description | Sequence analysis of structural variant breakpoints and experimental genotyping of inversions by PCR | ||||||||||||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 42 individuals (No genotypes available) |
| Comment | Inversion genotyped in 42 individuals of diverse origin (39 STD alleles/45 INV alleles) |
| Method | Genotype predicted by tag-SNPs |
| Status | Genotyping |
| Genotyping | 207 individuals (No genotypes available) |
| Comment | Inversion genotypes estimated from association with tag SNP rs1525303 (r2 > 0.8) |
| Description | Identification of human inversion polymorphisms by comparative analysis of human and chimpanzee genome sequence assemblies | ||||||||||||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 10 individuals (No genotypes available) |
| Comment | Inversion genotyped in 10 CEPH individuals (including 4 INV/INV) |
| Method | Genotype predicted by tag-SNPs |
| Status | Genotyping |
| Genotyping | 95 individuals (No genotypes available) |
| Comment | Inversion genotypes estimated from association with tag SNP rs1464853, rs1464851, and rs1525303 (r2 = 1) |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
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All samples and studies | 4 | 0 | 1.0000 | 0.0000 | NA |
| Africa (AFR)
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Africa (AFR) summary | 4 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
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All samples and studies | 61 | 84 | 0.3115 | 0.6885 | > 0.5 |
| Europe (EUR)
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Europe (EUR) summary | 61 | 84 | 0.3115 | 0.6885 | > 0.5 |
|---|
+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
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All samples and studies | 1 | 2 | 0.0000 | 1.0000 | NA |
| Japanese
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All samples and studies | 1 | 2 | 0.0000 | 1.0000 | NA |
| East Asia (EAS)
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East Asia (EAS) summary | 2 | 4 | 0.0000 | 1.0000 | NA |
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+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
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Unknown (Vicente-Salvador et al. 2017) | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
| Unknown
|
Unknown summary | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
|---|
+ Breakpoints
| Breakpoint 1 | chr7:70058904-70064121 | Breakpoint 2 | chr7:70076816-70076823 | ||
| Study | Vicente-Salvador et al. 2017 | ||||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly and two sequenced fosmids | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
FoSTeS
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| Flexibility | 10.35 | GC content | 0.32 | Stability | 1.78 |
| Comments |
Inverted region is flanked by a 5.2 kb deletion and a 6 bp duplication, and was probably generated by two fork stalling and template switching (FoSTeS) events, at least one of which was mediated by microhomology. Breakpoint positions comprise the deleted and the duplicated sequence. |
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+ Evolutionary history
| Ancestral allele | Standard | Age | ND |
| Derived allele | Inverted | Origin | ND |
+ Orientation in other species
| Species | Orientation | Method | Study |
| Chimpanzee | Standard | Genome sequence comparison | Feuk et al. 2005 |
| Chimpanzee | Standard | Polymerase chain reaction (PCR) | Pang et al. 2013 |
| Orangutan | Standard | Polymerase chain reaction (PCR) | Pang et al. 2013 |
| Chimpanzee | Standard | Polymerase chain reaction (PCR) | Vicente-Salvador et al. 2017 |
| Gorilla | Standard | Polymerase chain reaction (PCR) | Vicente-Salvador et al. 2017 |
| Rhesus macaque | Standard | Genome sequence comparison | Vicente-Salvador et al. 2017 |
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
HsInv1050 and HsInv1052 merge into HsInv1053
- 2018-11-06 15:31:56
| Breakpoint 1 | chr7:70058904-70064121 | Breakpoint 2 | chr7:70076816-70076823 |
| Study | Vicente-Salvador et al. 2017 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly and two sequenced fosmids | ||
| Definition method | Manual curation | ||
- 2017-09-29 00:00:00
| Breakpoint 1 | chr7:70053910-70063735 | Breakpoint 2 | chr7:70071888-70081828 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-09-29 00:00:00
| Breakpoint 1 | chr7:70059117-70063735 | Breakpoint 2 | chr7:70071888-70081809 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-09-18 00:00:00
| Breakpoint 1 | chr7:70053735-70063735 | Breakpoint 2 | chr7:70071888-70081888 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:15:27
| Breakpoint 1 | chr7:70031528-70066512 | Breakpoint 2 | chr7:70075724-70106476 |
| Assembly | hg18 | ||
| Description | Breakpoints not refined due to lack of overlap of predictions in at least one breakpoint | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:15:27
| Breakpoint 1 | chr7:70058904-70064121 | Breakpoint 2 | chr7:70076816-70076823 |
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly and two fosmid sequences | ||
| Definition method | Manual curation | ||
Hosted by the Comparative and Functional Genomics group at the Hospital del Mar Research Institute
Contact us at invfestdb@researchmar.net
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