Method for diagnosing a genetic alteration associated with a chromosomal locus

Abstract

Methods and apparatuses for selecting and arranging clinically relevant chromosomal loci allow an exemplary diagnostic array to simultaneously test for numerous genetic alterations that occur in many different parts of the human genome. Clinically irrelevant or ineffective loci are eliminated. One implementation increases reliability and accuracy by dividing the base-pair sequence of each chromosomal locus into segments and then assigning nucleic acid clones for comparative genomic hybridization to each different segment. The segments may overlap for increased resolution and control. Clones representing segments that are adjacent on a native chromosome are placed in non-adjacent target areas of the array to avoid interfering hybridization reactions. Arrangement motifs within an array may be redundantly repeated for high availability and increased reliability and accuracy of results. Techniques, hardware, software, logic engines, loci collections, and diagnostic arrays are described.

1 . A method, comprising:
 selecting a chromosomal locus for diagnosing a genetic alteration associated with the locus, wherein the chromosomal locus possesses at least a diagnostic base-pair sequence part of the chromosomal locus;   dividing the diagnostic base-pair sequence into multiple segments;   assigning one or more nucleic acid clones to represent each of the multiple segments; and   separately testing each segment via respective nucleic acid clones for at least part of the genetic alteration.   
   
   
       2 . The method as recited in  claim 1 , wherein each nucleic acid clone comprises one of a bacterial artificial chromosome, a yeast artificial chromosome, a P1-derived artificial chromosome, a cosmid, a plasmid, a fosmid, or a piece of cDNA. 
   
   
       3 . The method as recited in  claim 1 , wherein each nucleic acid clone is verified for association with the respective diagnostic base-pair sequence before selecting the nucleic acid clone to represent at least part of a segment of the diagnostic base-pair sequence. 
   
   
       4 . The method as recited in  claim 1 , wherein separately testing comprises fluorescence in situ hybridization. 
   
   
       5 . The method as recited in  claim 1 , further comprising:
 selecting a genetic region in a chromosomal vicinity of the chromosomal locus;   dividing the genetic region into multiple regional segments; and   individually testing each regional segment to derive information about an alteration of the chromosomal locus.   
   
   
       6 . The method as recited in  claim 1 , further comprising selecting a reference base-pair sequence not associated with the genetic alteration as a comparison reference for diagnosing the genetic alteration of the chromosomal locus;
 assigning nucleic acid clones to represent the reference base-pair sequence;   comparing the reference base-pair sequence with the segments of the diagnostic base-pair sequence to derive information about an alteration of the chromosomal locus.   
   
   
       7 . The method as recited in  claim 1 , wherein separately testing comprises at least spatially isolating the nucleic acid clones assigned to each segment on an array. 
   
   
       8 . The method as recited in  claim 7 , wherein the array comprises a comparative genomic hybridization array. 
   
   
       9 . The method as recited in  claim 7 , further comprising:
 selecting a reference base-pair sequence not associated with the genetic alteration being diagnosed as a reference for comparison with test results of the diagnostic base-pair sequence; and   on the array, flanking a target area for at least one of the segments of the diagnostic base-pair sequence with a target area for the reference base-pair sequence.   
   
   
       10 . The method as recited in  claim 1 , further comprising:
 using multiple target areas of an array to redundantly test one of the segments;   dividing the array into multiple sub-arrays;   including one of the multiple target areas for the redundant testing in each of the multiple sub-arrays of the array;   introducing a design in the array for correct orientation of the array during testing; and   printing the array in a non-symmetrical pattern to allow the correct orientation of the array.   
   
   
       11 . The method as recited in  claim 10 , wherein the array is redundantly reproduced for comparison of test results between the redundantly reproduced arrays. 
   
   
       12 . The method as recited in  claim 1 , further comprising collating a test result for each segment into a test result for the diagnostic base-pair sequence, wherein the collated test results are capable of supporting a diagnosis concerning genetic alteration of the chromosomal locus. 
   
   
       13 . The method as recited in  claim 12 , wherein the segments overlap in coverage of a part of a base-pair sequence; and
 a segment overlap is filtered from the collated test results.   
   
   
       14 . A method, comprising:
 selecting a chromosomal locus for diagnosing a genetic alteration associated with the locus, wherein the chromosomal locus possesses at least a diagnostic base-pair sequence part of the chromosomal locus;   dividing the diagnostic base-pair sequence into multiple segments;   assigning one or more oligomers to represent each of the multiple segments; and   separately testing each segment via respective oligomers for at least part of the genetic alteration.   
   
   
       15 . The method as recited in  claim 14 , further comprising synthesizing each of the oligomers. 
   
   
       16 . The method as recited in  claim 14 , wherein each oligomer is verified for association with the respective diagnostic base-pair sequence before synthesizing the oligomer to represent at least part of a segment of the diagnostic base-pair sequence. 
   
   
       17 . The method as recited in  claim 14 , wherein separately testing comprises fluorescence in situ hybridization. 
   
   
       18 . The method as recited in  claim 14 , further comprising:
 selecting a genetic region in a chromosomal vicinity of the chromosomal locus;   dividing the genetic region into multiple regional segments to be represented by the oligomers; and   individually testing each regional segment to derive information about an alteration of the chromosomal locus.   
   
   
       19 . The method as recited in  claim 14 , further comprising selecting a reference base-pair sequence not associated with the genetic alteration as a comparison reference for diagnosing the genetic alteration of the chromosomal locus;
 assigning oligomers to represent the reference base-pair sequence;   comparing the reference base-pair sequence with the segments of the diagnostic base-pair sequence to derive information about an alteration of the chromosomal locus.   
   
   
       20 . The method as recited in  claim 14 , wherein separately testing comprises at least spatially isolating oligomers representing each segment on an array.