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High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE49447 | GEO | 2013/08/02

SECONDARY ACCESSION(S): PRJNA213937

REPOSITORIES: GEO

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High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-02 | E-GEOD-49447 | biostudies-arrayexpress

High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain (part 2)

Project description:The goal of this experiment was to determine the size, genomic extent and gene content of each Xq28 rearrangement.

2013-08-02 | GSE49446 | GEO

High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain (part 1)

Project description:The goal of this experiment was to determine the size, genomic extent and gene content of each Xq28 rearrangement.

2013-08-02 | GSE49440 | GEO

High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain (part 1)

Project description:The goal of this experiment was to determine the size, genomic extent and gene content of each Xq28 rearrangement. We designed a tiling-path oligonucleotide microarray spanning 4.6 Mb surrounding the MECP2 region on Xq28. The custom 4x44k Agilent Technologies microarray was designed using the Agilent earray website. We selected 22,000 probes covering ChrX: 150,000,000-154,600,000 (NCBI build 36), including the MECP2 gene, which represents an average distribution of 1 probe per 209 bp. Each patient sample was run once using this array; hybridization was done using a gender-matched reference sample.

2013-08-02 | E-GEOD-49440 | biostudies-arrayexpress

High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain (part 2)

Project description:The goal of this experiment was to determine the size, genomic extent and gene content of each Xq28 rearrangement. We designed a tiling-path oligonucleotide microarray spanning 4.0 Mb surrounding the MECP2 region on Xq28. The custom 4x44k Agilent Technologies microarray was designed using the Agilent earray website. We selected 22,000 probes covering ChrX: 150,400,000-154,400,000 (NCBI build 35), including the MECP2 gene, which represents an average distribution of 1 probe per 500 bp. Each patient sample was run once using this array; hybridization was done using a gender-matched reference sample.

2013-08-02 | E-GEOD-49446 | biostudies-arrayexpress

High-resolution custom array spanning Xq22 region to study patients carrying PLP1 copy number gain

Project description:We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array and breakpoint junction sequence analysis. Analysis of these data enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated. Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array and breakpoint junction sequence analysis.

2019-10-09 | GSE138542 | GEO

High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain

Project description:High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain

| PRJNA213937 | ENA

High-resolution custom array spanning Xq22 region to study patients carrying PLP1 copy number gain

Project description:High-resolution custom array spanning Xq22 region to study patients carrying PLP1 copy number gain

| PRJNA576488 | ENA

High-resolution custom array spanning short arm of chromosome 17

Project description:The goal of this experiment was to determine the size, genomic extent and gene content of rearrangements involving 17p.

2014-11-01 | GSE62004 | GEO

A custom ddPCR method for the detection of copy number variations in the nebulin triplicate region.

Project description:The human genome contains repetitive regions, such as segmental duplications, known to be prone to copy number variation. Segmental duplications are highly identical and homologous sequences, posing a specific challenge for most mutation detection methods. The giant nebulin gene is expressed in skeletal muscle. It harbors a large segmental duplication region composed of eight exons repeated three times, the so-called triplicate region. Mutations in nebulin are known to cause nemaline myopathy and other congenital myopathies. Using our custom targeted Comparative Genomic Hybridization arrays, we have previously shown that copy number variations in the nebulin triplicate region are pathogenic when the copy number of the segmental duplication block deviates two or more copies from the normal number, which is three per allele. To complement our Comparative Genomic Hybridization arrays, we have established a custom Droplet Digital PCR method for the detection of copy number variations within the nebulin triplicate region. The custom Droplet Digital PCR assays allow sensitive, rapid, high-throughput, and cost-effective detection of copy number variations within this region and is ready for implementation a screening method for disease-causing copy number variations of the nebulin triplicate region. We suggest that Droplet Digital PCR may also be used in the study and diagnostics of other segmental duplication regions of the genome.

| S-EPMC9109913 | biostudies-literature

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