Changes

The laboratory should choose a microarray design with probe coverage suitable for detection of known copy-number aberrations associated with the neoplasm of interest. Microarray platform design may be (i) targeted to specific regions of the genome for detection of known cancer-associated unbalanced genomic alterations, (ii) genome-wide with a specified distribution and spacing of probes, or (iii) both targeted and genome-wide, with varying distribution and spacing of probes in specific regions and across the entire genome.

The laboratory should choose a microarray design with probe coverage suitable for detection of known copy-number aberrations associated with the neoplasm of interest. Microarray platform design may be (i) targeted to specific regions of the genome for detection of known cancer-associated unbalanced genomic alterations, (ii) genome-wide with a specified distribution and spacing of probes, or (iii) both targeted and genome-wide, with varying distribution and spacing of probes in specific regions and across the entire genome.

Manufacturers of microarrays should verify the identity of each clone or probe on the platform used for clinical testing. Probes selected from the public domain should be listed with their physical and cytogenetic positions on the human genome. All probe descriptions and annotations should be openly accessible. Details regarding the microarray design, the synthesis verification, and all quality control (QC) steps taken to validate and assess the performance and reproducibility of the microarray should be documented and provided by the manufacturer. Additional information may be found in the American College of Medical Genetics and Genomics recommendations for the design and performance expectations for clinical genomic copy-number microarray devices.28

Manufacturers of microarrays should verify the identity of each clone or probe on the platform used for clinical testing. Probes selected from the public domain should be listed with their physical and cytogenetic positions on the human genome. All probe descriptions and annotations should be openly accessible. Details regarding the microarray design, the synthesis verification, and all quality control (QC) steps taken to validate and assess the performance and reproducibility of the microarray should be documented and provided by the manufacturer. Additional information may be found in the American College of Medical Genetics and Genomics recommendations for the design and performance expectations for clinical genomic copy-number microarray devices.<ref>Kearney HM, South ST, Wolff DJ, Lamb A, Hamosh A, Rao KW; Working Group of the American College of Medical Genetics. American College of Medical Genetics recommendations for the design and performance expectations for clinical genomic copy number microarrays intended for use in the postnatal setting for detection of constitutional abnormalities. Genet Med 2011;13:676–679.</ref>

Microarrays should be designed with consideration of the statistical algorithms to be used for determining abnormal thresholds. The number and density of probes within a given region of interest, i.e., within a region known to be associated with a cancer gene or feature, should provide the sensitivity needed for detection of a copy-number variation.

Microarrays should be designed with consideration of the statistical algorithms to be used for determining abnormal thresholds. The number and density of probes within a given region of interest, i.e., within a region known to be associated with a cancer gene or feature, should provide the sensitivity needed for detection of a copy-number variation.