Prenatal Microarray Testing

Microarray-based Comparative Genomic Hybridization (aCGH) 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+SNP Analysis

Clinical Indications For Prenatal CGH+SNP Analysis

  • Follow-up of de novo, apparently balanced rearrangements detected by karyotyping
  • Pregnancy with a suspicion of an imbalance in a specific genomic region
  • Abnormal ultrasound findings
  • Family history of a known or suspected chromosomal abnormality
  • Identification of a mosaic chromosome imbalance, such as a marker chromosome observed by karyotyping
  • Stillbirth/fetal loss
  • Pregnancy with suspected UPD/conditions associated with imprinting
  • Pregnancy with autosomal recessive condition due to suspected common ancestry or consanguinuity

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

  • Pregnancy with suspected X chromosome contiguous gene deletion/duplication syndrome
  • Pregnancy with a marker/ring of X chromosome
  • Pregnancy with X;autosome translocation
  • Pregnancy with suspected X-linked genetic disorder
  • Suspected ambiguous genitalia detected by prenatal ultrasound
  • Family history of X-linked genetic disorder

Platform For X-HR Analysis

We use the Agilent 180K oligonucleotide array platform, which was constructed by the UPMC Cytogenetics Laboratory for the sole purpose of identifying DNA copy number gains and losses associated with X chromosome imbalances. The 180,000 oligonucleotides on the X-HR chip cover the 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 in 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 and Disorders Detected Document

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

Requirements Document and Requisition Form

Use Adobe Acrobat to print the PDF forms.

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%)

Prenatal Microarray Testing

Microarray-based Comparative Genomic Hybridization (aCGH) 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+SNP Analysis

Clinical Indications For Prenatal CGH+SNP Analysis

  • Follow-up of de novo, apparently balanced rearrangements detected by karyotyping
  • Pregnancy with a suspicion of an imbalance in a specific genomic region
  • Abnormal ultrasound findings
  • Family history of a known or suspected chromosomal abnormality
  • Identification of a mosaic chromosome imbalance, such as a marker chromosome observed by karyotyping
  • Stillbirth/fetal loss
  • Pregnancy with suspected UPD/conditions associated with imprinting
  • Pregnancy with autosomal recessive condition due to suspected common ancestry or consanguinuity

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

  • Pregnancy with suspected X chromosome contiguous gene deletion/duplication syndrome
  • Pregnancy with a marker/ring of X chromosome
  • Pregnancy with X;autosome translocation
  • Pregnancy with suspected X-linked genetic disorder
  • Suspected ambiguous genitalia detected by prenatal ultrasound
  • Family history of X-linked genetic disorder

Platform For X-HR Analysis

We use the Agilent 180K oligonucleotide array platform, which was constructed by the UPMC Cytogenetics Laboratory for the sole purpose of identifying DNA copy number gains and losses associated with X chromosome imbalances. The 180,000 oligonucleotides on the X-HR chip cover the 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 in 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 and Disorders Detected Document

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

Requirements Document and Requisition Form

Use Adobe Acrobat to print the PDF forms.

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%)

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