upmc   PITTSBURGH CYTOGENETICS LABORATORY

 

LABORATORY SERVICES

 

PRENATAL 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 CGH+SNP and high resolution X-chromosome (X-HR) microarray analyses for prenatal samples.

WHOLE GENOME CGH+SNPANALYSIS

CLINICAL INDICATIONS FOR PRENATAL CGH+SNP 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, February 2009).

HIGH RESOLUTION X-CHROMOSOME MICROARRAY ANALYSIS (X-HR)

CLINICAL INDICATION FOR PRENATAL X-HR ANALYSIS

PLATFORM FOR X-HR ANALYSIS

We 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 1-2 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

SPECIMEN REQUIREMENTS

PRENATAL DIAGNOSIS (microarray, FISH and K-type)
Specimen Types Requirements
Chorionic villi Minimum 15-25mg of chorionic villus tissue in a sterile tube containing culture medium, sterile saline or balanced salt solution
Amniotic Fluid Minimum 25–30cc of the fluid
Parental peripheral blood 1 green top tube (1 x NaHep) and one purple top tube (1XEDTA) , each containing 5 cc whole blood

 

SPECIMEN REQUIRMENTS (PDF TABLE)

CONSTITUTIONAL STUDY REQUISITION FORM (PDF TABLE)

ADVANTAGES AND LIMITATIONS FOR THE TESTS

CGH-SNP can:

  • detect chromosome imbalances identified by classical chromosome analysis.
  • detect chromosome imbalances that cannot be identified by chromosome analysis.
  • simultaneously and rapidly evaluate thousands of loci for copy number imbalances.
  • further characterize the chromosome imbalances detected by karyotyping (e.g., maker chromosomes).
  • detect absence of heterozygosity (AOH) and uniparental isodisomy (UPD).
  • detect polyploidies

CGH-SNP cannot detect:

  • balanced rearrangements (e.g., balanced translocation, inversion).
  • base pair mutations.
  • gains or losses in the regions of the genome not covered by array.
  • low level mosaicism (<20%).