A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications.
We have constructed the first comprehensive microarray representing a human chromosome for analysis of DNA copy number variation. This chromosome 22 array covers 34.7 Mb, representing 1.1% of the genome, with an average resolution of 75 kb. To demonstrate the utility of the array, we have applied it to profile acral melanoma, dermatofibrosarcoma, DiGeorge syndrome and neurofibromatosis 2. We accurately diagnosed homozygous/heterozygous deletions, amplifications/gains, IGLV/IGLC locus instability, and breakpoints of an imbalanced translocation. We further identified the 14-3-3 eta isoform as a candidate tumor suppressor in glioblastoma. Two significant methodological advances in array construction were also developed and validated. These include a strictly sequence defined, repeat-free, and non-redundant strategy for array preparation. This approach allows an increase in array resolution and analysis of any locus; disregarding common repeats, genomic clone availability and sequence redundancy. In addition, we report that the application of phi29 DNA polymerase is advantageous in microarray preparation. A broad spectrum of issues in medical research and diagnostics can be approached using the array. This well annotated and gene-rich autosome contains numerous uncharacterized disease genes. It is therefore crucial to associate these genes to specific 22q-related conditions and this array will be instrumental towards this goal. Furthermore, comprehensive epigenetic profiling of 22q-located genes and high-resolution analysis of replication timing across the entire chromosome can be studied using our array.
Buckley
Patrick G
PG
Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, 751 85 Uppsala, Sweden
Mantripragada
Kiran K
KK
Benetkiewicz
Magdalena
M
Tapia-Páez
Isabel
I
Diaz De Ståhl
Teresita
T
Rosenquist
Magnus
M
Ali
Haider
H
Jarbo
Caroline
C
De Bustos
Cecilía
C
Hirvelä
Carina
C
Sinder Wilén
Birgitta
B
Fransson
Ingegerd
I
Thyr
Charlotte
C
Johnsson
Britt-Inger
BI
Bruder
Carl E G
CE
Menzel
Uwe
U
Hergersberg
Martin
M
Mandahl
Nils
N
Blennow
Elisabeth
E
Wedell
Anna
A
Beare
David M
DM
Collins
John E
JE
Dunham
Ian
I
Albertson
Donna
D
Pinkel
Daniel
D
Bastian
Boris C
BC
Faruqi
A Fawad
AF
Lasken
Roger S
RS
Ichimura
Koichi
K
Collins
V Peter
VP
Dumanski
Jan P
JP
D002874:Chromosome Mapping / Q000379:methods; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics*; D005260:Female; D005784:Gene Amplification / Q000235:genetics; D017353:Gene Deletion; D018628:Gene Dosage; D016147:Genes, Tumor Suppressor; D023281:Genomics / Q000379:methods*; D006801:Humans; D008297:Male; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*