Inversion Report: HsInv0544

Human Polymorphic Inversion DataBase

Inversion Report: HsInv0544

General information

Accession	HsInv0544	Region of the inversion	chr15:72140038-73384192
Status	Validated	Prediction type	Complex
Estimated Inversion Size	1,214,103 bp	Supporting predictions	4
Inverted allele frequency	0.0185	Mechanism of origin	NAHR
Functional effect	Intergenic breakpoints	Breakpoint 1	chr15:72140038-72170064
Ancestral orientation	Standard	Breakpoint 2	chr15:73354113-73384192

- Region map

+ Predictions

- 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	chr15:72140039-72170064	Breakpoint 2	chr15:73354114-73384192
Individuals
Comments	Breakpoints defined by INVFEST based on the analysis of discordant fosmid ABC14_1078822_N5 paired end mapping data

- 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

chr15:72147611-72156474

Breakpoint 2

chr15:73376398-73382843

D/C Score

-5.78

Disc. Support Prob.

Support

4 probes

Individuals

NA12156	NA12878	NA15510	NA18507	NA18517	NA18555	NA18956	NA19129	NA19240

Comments

Below the threshold of the Discordant/Concordant (D/C) ratio score. Below the threshold of the Discordant Support (DS) probability

Name

Breakpoint 1

chr15:72155143-72200637

Breakpoint 2

chr15:73355356-73400850

D/C Score

Disc. Support Prob.

Support

3 probes

Individuals

NA12156	NA12878	NA15510	NA18507	NA18517	NA18555	NA18956	NA19129	NA19240

Comments

Below the threshold of the Discordant Support (DS) probability

Name

Breakpoint 1

chr15:72139406-72185407

Breakpoint 2

chr15:73304979-73352888

D/C Score

Disc. Support Prob.

Support

5 probes

Individuals

NA12156	NA12878	NA15510	NA18507	NA18517	NA18555	NA18956	NA19129	NA19240

Comments

prediction outside of the current location of the inversion breakpoints

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 26 STD/STD - 1 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.

-INVFEST curation

Description

Information update by manual analysis of InvFEST curators

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	0	1.0000	0.0000	NA

Africa (AFR)	Africa (AFR) summary	11	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	Utah residents with Northern and Western European ancestry (CEU) (Antonacci et al. 2009)	8	0	1.0000	0.0000	NA

Europe (EUR)	Europe (EUR) summary	8	0	1.0000	0.0000	NA

+ 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	1	0.8750	0.1250	> 0.5
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	1	0.9375	0.0625	> 0.5

+ Breakpoints

Breakpoint 1	chr15:72140038-72170064	Breakpoint 2	chr15:73354113-73384192
Study	INVFEST curation
Description	Breakpoints defined by InvFEST curators as the inverted segmental duplications
Definition method	Manual curation
Mechanism of origin	NAHR

Flexibility

9.98

GC content

0.54

Stability

2.01

Comments

Inversion generated by non-allelic homologous recombination (NAHR) between 30 kb inverted SDs with 98.8% identity

Sequence features

Segmental duplications:

Position SD1	Size (bp)	Position SD2	Size (bp)	Identity	Relative orientation
chr15:72140038-72170064	30,027	chr15:73354113-73384192	30,080	0.990	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

Breakpoint 1	chr15:72131140-72197406	Breakpoint 2	chr15:73303288-73402434
Assembly	hg18
Definition method	Default informatic definition

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

Breakpoint 1	chr15:72155143-72156474	Breakpoint 2	chr15:73376398-73382843
Assembly	hg18
Definition method	Default informatic definition

Breakpoint 1	chr15:72147611-72200637	Breakpoint 2	chr15:73355356-73400850
Assembly	hg18
Description	Breakpoints not refined due to lack of overlap of predictions in at least one breakpoint. Breakpoints calculated without considering unreliable predictions
Definition method	Default informatic definition