Methods and apparatuses for comparative genomic microarray analysis
OwnerBlake C. Ballif, Lisa G. Shaffer +1inventors
InventorsBlake C. Ballif, Lisa G. Shaffer, Bassem A. Bejjani
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Abstract
Control nucleic acids and their method of use to simultaneously test for numerous genetic alterations that involve an unbalanced arrangement of chromosomes. One implementation increases reliability and accuracy by adding additional nucleic acid to test and/or reference samples. Clones representing segments insensitive to chromosomal rearrangements are placed in non-adjacent target areas of a microarray to avoid interfering hybridization reactions.
Claims32
An array for the detection of aneuploidy that comprises a first plurality of nucleic acid segments corresponding to a first set of chromosomal loci wherein each chromosomal locus is capable of genetic alteration indicative of a copy number and a second plurality of nucleic acid segments corresponding to a second set of chromosomal loci that are not associated with the copy number being detected, wherein each of the first and second plurality of nucleic acid segments represents a portion of the base-pair sequence of a chromosomal locus;
- wherein each nucleic acid segment is immobilized to a discrete and known spot on a substrate surface to form an array of nucleic acids, wherein the nucleic acid segments representing chromosomal loci that are adjacent on a native chromosome are placed in non-adjacent target areas of the array.
A set of control nucleic acids for use in comparative genomic hybridization analysis wherein the nucleic acids are derived from a naturally occurring sample that comprises a known aneuploidy.
A set of control nucleic acids for use in comparative genomic hybridization analysis wherein the nucleic acids are comprised of a mixture of known amounts of cloned nucleic acid segments corresponding to a plurality of chromosomal loci derived from a biological sample.
A set of control nucleic acids for use in comparative genomic hybridization analysis that comprises a first group of a known amount of nucleic acid segments added to a test sample and a second group of a known amount of substantially identical nucleic acid segments added to a reference sample.
A method of comparative genomic hybridization analysis that comprises the following steps:
- (a) providing an array comprising a plurality of nucleic acid target elements, wherein each nucleic acid target element is comprised of a nucleic acid segment that is immobilized to a discrete and known spot on a substrate surface to form an array and the nucleic acid segments comprise a substantially complete first genome of a known mammalian karyotype;
- (b) providing a first sample, wherein the sample comprises a plurality of genomic nucleic acid segments comprising a substantially complete complement of a first genome labeled with a first detectable label;
- (c) providing a second sample, wherein the sample comprises a plurality of genomic nucleic acid labeled with a second detectable label, and the genomic nucleic acid sample comprises a substantially complete complement of genomic nucleic acid of a cell or a tissue sample, and the karyotype of the second sample comprises a known abnormal karyotype;
- (d) contacting the samples with the array of step (a) under conditions wherein the nucleic acid in the samples can specifically hybridize to the genomic nucleic acid segments immobilized on the array;
- (e) measuring the amount of first and second detectable label on each spot after the contacting of step (d) and determining the karyotype of the first sample by comparative genomic hybridization.
Dependencies are inferred from the claim text.