Inversion Report: HsInv0264

Human Polymorphic Inversion DataBase

Inversion Report: HsInv0264

General information

Accession	HsInv0264	Region of the inversion	chr3:196830755-198878785
Status	Validated	Prediction type	Complex
Estimated Inversion Size	1,998,436 bp	Supporting predictions	3
Inverted allele frequency	0.0741	Mechanism of origin	NAHR
Functional effect	Intergenic breakpoints	Breakpoint 1	chr3:196830755-196880220
Ancestral orientation	Standard	Breakpoint 2	chr3:198829061-198878785

- Region map

+ Predictions

- Pang et al. 2010

Description	Paired-end mapping analysis of the J. Craig Venter genome (HuRef)
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chr3:196807769-196845584

Breakpoint 2

chr3:198872078-198913353

Individuals

HuRef

- Antonacci et al. 2009

Description	Characterization of six large inversion polymorphisms with complex segmental duplications at the breakpoints in 27 individuals from three HapMap populations by a metaphase FISH-based assay
Method	Fluorescence in situ hybridization (FISH)

Name
Breakpoint 1	chr3:196830752-196880220	Breakpoint 2	chr3:198829061-198878785
Individuals
Comments	The closing of the 100-kb gap next to Breakpoint (BP) 1 found in HG17 genome assembly in the more recent HG19 assembly generates 45.5-kb (BP1) and 49.7-kb (BP2) segmental duplications at the inversion breakpoints (instead of the 15.5-kb in HG17 and HG18) that modify the previous Antonacci et al. 2009 breakpoint definition. The curated HG19 breakpoint coordinates have been translated into HG18 genome assembly coordinates.

- 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

chr3:196846872-196875460

Breakpoint 2

chr3:198829561-198858582

D/C Score

-2.12

Disc. Support Prob.

Support

11 probes

Individuals

NA12156	NA12878	NA15510	NA18507	NA18517	NA18555	NA18956	NA19129	NA19240

Comments

Below the threshold of the Discordant Support (DS) probability

+ Validation and genotyping

-Antonacci et al. 2009

Description

Characterization of six large inversion polymorphisms with complex segmental duplications at the breakpoints in 27 individuals from three HapMap populations by a metaphase FISH-based assay

Method	Fluorescence in situ hybridization (FISH)
Status	Validated
Genotyping	27 individuals: 27 HapMap/1000GP 23 STD/STD - 4 STD/INV

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

Please be aware that this information will be displayed in the Frequency section of the Inversion report, but the following will not be available: Hardy-Weinberg test and genotype file for download. Also, data will not be averaged with other studies of the same population.

Population
Analyzed individuals
Inverted alleles
Standard frequency
Inverted frequency

+ Manually curated breakpoints:

Only modified sections are submitted. All the corresponding fields must be complete because they will be overwritten. In the Frequency without genotypes section multiple populations can be added if the editing process is repeated for each one of them.

-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	Sequence analysis
Status	Breakpoint refinement

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

+ Manually curated breakpoints:

- Frequency

+ Africa (AFR)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Yoruba	Yoruba in Ibadan, Nigeria (YRI) (Antonacci et al. 2009)	11	2	0.9091	0.0909	> 0.5

Africa (AFR)	Africa (AFR) summary	11	2	0.9091	0.0909	> 0.5

+ Europe (EUR)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Northwestern European	Utah residents with Northern and Western European ancestry (CEU) (Antonacci et al. 2009)	8	2	0.8750	0.1250	> 0.5

Europe (EUR)	Europe (EUR) summary	8	2	0.8750	0.1250	> 0.5

+ East Asia (EAS)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Han Chinese	Han Chinese in Beijing, China (CHB) (Antonacci et al. 2009)	4	0	1.0000	0.0000	NA
Japanese	Japanese in Tokyo, Japan (JPT) (Antonacci et al. 2009)	4	0	1.0000	0.0000	NA

East Asia (EAS)	East Asia (EAS) summary	8	0	1.0000	0.0000	NA

+ Breakpoints

Breakpoint 1	chr3:196830755-196880220	Breakpoint 2	chr3:198829061-198878785
Study	Martinez-Fundichely et al. 2014 (in preparation)
Description	Breakpoints defined as the most identical inverted segmental duplications
Definition method	Manual curation
Mechanism of origin	NAHR

Flexibility

GC content

0.29

Stability

1.02

Comments

Inversion generated by non-allelic homologous recombination (NAHR) between 46-50 kb inverted SDs with 99% identity

Sequence features

Segmental duplications:

Position SD1	Size (bp)	Position SD2	Size (bp)	Identity	Relative orientation
chr3:196830752-196837663	6,912	chr3:198871831-198878785	6,955	0.990	Inverted
chr3:196864664-196880220	15,557	chr3:198829061-198844608	15,548	0.986	Inverted

+ Evolutionary history

+ Functional effects

+ Report history

Hosted by the Comparative and Functional Genomics group at the Hospital del Mar Research Institute

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Ancestral allele	Standard	Age	ND
Derived allele	Inverted	Origin	ND

Species	Orientation	Method	Study
Chimpanzee	Standard	Fluorescence in situ hybridization (FISH)	Antonacci et al. 2009
Bonobo	Standard	Fluorescence in situ hybridization (FISH)	Antonacci et al. 2009
Gorilla	Standard	Fluorescence in situ hybridization (FISH)	Antonacci et al. 2009
Orangutan	Standard	Fluorescence in situ hybridization (FISH)	Antonacci et al. 2009