Inversion Report: HsInv0032

Human Polymorphic Inversion DataBase

Inversion Report: HsInv0032

General information

Accession	HsInv0032	Region of the inversion	chr17:5826333-5827698
Status	Validated	Prediction type	Simple
Estimated Inversion Size	1,111 bp	Supporting predictions	6
Inverted allele frequency	ND	Mechanism of origin	NAHR
Functional effect	Intergenic breakpoints	Breakpoint 1	chr17:5826333-5826588
Ancestral orientation	NA	Breakpoint 2	chr17:5827443-5827698

- Region map

+ Predictions

- Chaisson et al. 2015

Description	Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1)
Method	Long-read sequencing

Name

Breakpoint 1

chr17:5826165-5826165

Breakpoint 2

chr17:5827865-5827865

Individuals

CHM1

- Pang et al. 2010

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

Name

Breakpoint 1

chr17:5825790-5826431

Breakpoint 2

chr17:5827573-5829136

Individuals

HuRef

- McKernan et al. 2009

Description	Next generation sequencing and analysis by paired-end mapping of an individual genome of African origin
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chr17:5826357-5826545

Breakpoint 2

chr17:5827449-5827816

Individuals

NA18507

- Korbel et al. 2007

Description	Paired-end mapping of 3-kb fragments in an African and in a putatively European individual with some predictions validated by PCR, fiber-FISH or comparison with Celera assembly
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chr17:5827502-5827502

Breakpoint 2

chr17:5829860-5829860

Individuals

NA15510	NA18505

- Levy et al. 2007

Description	Sequencing and analysis of the independently assembled diploid J. Craig Venter genome (HuRef)
Method	Genome sequence comparison

Name

Breakpoint 1

chr17:5826739-5826739

Breakpoint 2

chr17:5827291-5827291

Individuals

HuRef

- 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

chr17:5790343-5826894

Breakpoint 2

chr17:5827293-5863576

D/C Score

Disc. Support Prob.

0.99966

Support

3 probes

Individuals

NA12156	NA12878	NA15510	NA18507	NA18517	NA18555	NA18956	NA19129	NA19240

+ Validation and genotyping

-Vicente-Salvador et al. 2017

Description

Validation and characterization of human inversions predicted by comparison of two independently assembled human genomes

Method	Sequence analysis
Status	Breakpoint refinement

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.

-Chaisson et al. 2015

Description

Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1)

Method	Sequence analysis
Status	Validated
Comment	Inversion validated by analysis of CH17-278I9 BAC sequence (AC255460) obtained with PacBio long reads

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

+ Manually curated breakpoints:

+ Frequency

+ Breakpoints

Breakpoint 1	chr17:5826333-5826588	Breakpoint 2	chr17:5827443-5827698
Study	Vicente-Salvador et al. 2017
Description	Breakpoints defined by comparison with HuRef Human Genome assembly and a sequenced BAC
Definition method	Manual curation
Mechanism of origin	NAHR

Flexibility

10.14

GC content

0.46

Stability

1.9

Comments

Inversion generated by non-allelic homologous recombination (NAHR) between 0.7 kb inverted SDs practically in tandem with 97.8% identity

Sequence features

Segmental duplications:

Position SD1	Size (bp)	Position SD2	Size (bp)	Identity	Relative orientation
chr17:5826166-5827865	1,700	chr17:5826166-5827865	1,700	0.922	Inverted

Inverted repeats:

Position IR1	Size (bp)	Position IR2	Size (bp)	Identity	Relative orientation
chr17:5826163-5826882	720	chr17:5827149-5827868	720	97.8	Inverted

+ Evolutionary history

+ Functional effects

+ Report history

Hosted by the Comparative and Functional Genomics group at the Universitat Autònoma de Barcelona

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

Breakpoint 1	chr17:5825739-5826894	Breakpoint 2	chr17:5827293-5828291
Assembly	hg18
Definition method	Default informatic definition

Breakpoint 1	chr17:5825739-5826894	Breakpoint 2	chr17:5827293-5828291
Assembly	hg18
Definition method	Default informatic definition

Breakpoint 1	chr17:5825739-5826894	Breakpoint 2	chr17:5827293-5828291
Assembly	hg18
Definition method	Default informatic definition

Breakpoint 1	chr17:5825739-5826894	Breakpoint 2	chr17:5827293-5828291
Assembly	hg18
Definition method	Default informatic definition

Ancestral allele	NA	Age	ND
Derived allele	NA	Origin	ND