upmc   PITTSBURGH CYTOGENETICS LABORATORY

 

LABORATORY SERVICES

 

Postnatal Microarray Testing

Microarray-based Comparative Genomic Hybridization (aCGH) is a new genetic test that can detect both unbalanced genomic alterations usually identified by chromosome analysis (karyotyping) and unbalanced genomic alterations that cannot be identified by karyotyping (including microdeletions and microduplications and many single gene deletions or duplications). CGH+SNP microarrays can simultaneously detect copy number changes as well as copy neutral aberrations, such as absence of heterozygosity (AOH) and uniparental disomy (UPD).
We provide whole genome aCGH, CGH+SNP and high resolution X-chromosome (X-HR) microarray analyses.

WHOLE GENOME CGH+SNP ANALYSIS

CLINICAL INDICATIONS FOR POSTNATAL aCGH ANALYSIS

PLATFORM FOR CGH+SNP ANALYSIS

We use Agilent’s SurePrint G3 CGH+SNP microarrays (4x180K ISCA design) platform. The 110,712 (CGH) oligo probes and 59,647 (SNP) probes with 25.3 kb overall median probe spacing are throughout the genome and with 5 kb in ISCA regions. This platform is designed based on UCSC hg19 (NCBI Build 37, Februry 2009).

High resolution X-chromosome microarray analyses (X-HR)

CLINICAL INDICATION FOR POSTNATAL X-HR ANALYSIS

PLATFORM FOR X-HR ANALYSIS

Click to zoomWe use the Agilent 180K oligonucleotide array platform specifically designed and validated by Pittsburgh Cytogenetics Laboratory for the X-chromosome disorders. The 180,000 oligonucleotides on the X-HR chip cover entire X-chromosome genome with high density probes in the regions containing genes involved in X-chromosome disorders or associated with premature ovarian failure, as well as some autosomal genes involved disorders of sexual differentiation. The maximum probe spacing is one probe for every 1 Kb throughout the X-chromosome genome and one probe for every 0.3-0.5 Kb in the regions containing genes.

Genes Covered by X-HR and disorders detected by X-HR

SAMPLES FOR MICROARRAY ANALYSIS

DNA extracted from peripheral blood will be used for microarray testing. DNA can also be extracted from skin samples for the test.

SPECIMEN REQUIREMENTS

POSTNATAL AND ADULT (microarray, FISH and KARYOTYPING)
Specimen Types Requirements
Peripheral Blood 1 green top tube (1 x NaHep) and one purple top tube (1XEDTA) , each containing 5 cc whole blood
For infant or young children:
1 green top tube (1 x NaHep) and one purple top tube (1XEDTA) , each containing -1-3 cc whole blood
Parental peripheral blood 1 green top tube (1 x NaHep) and one purple top tube (1XEDTA) , each containing 5 cc whole blood

 

SPECIMEN REQUIREMENTS (PDF TABLE)

CONSITUTIONAL STUDY REQUISITION FORM (PDF TABLE)

ADVANTAGES AND LIMITATIONS FOR THE TESTS

CGH-SNP can :

aCGH cannot detect: