PMID- 21178330
OWN - NLM
STAT- MEDLINE
DCOM- 20110406
LR  - 20110210
IS  - 1424-859X (Electronic)
IS  - 1424-8581 (Linking)
VI  - 132
IP  - 4
DP  - 2011
TI  - Visualization of fine-scale genomic structure by oligonucleotide-based 
      high-resolution FISH.
PG  - 248-54
LID - 10.1159/000322717 [doi]
AB  - The discovery of complex structural variations that exist within individual 
      genomes has prompted a need to visualize chromosomes at a higher resolution than 
      previously possible. To address this concern, we established a robust, 
      high-resolution fluorescence in situ hybridization (FISH) method that utilizes 
      probes derived from high complexity libraries of long oligonucleotides (>150 
      mers) synthesized in massively parallel reactions. In silico selected 
      oligonucleotides, targeted to only the most informative elements in 18 genomic 
      regions of interest, eliminated the need for suppressive hybridization reagents. 
      Because of the inherent flexibility in our probe design methods, we readily 
      visualized regions as small as 6.7 kb with high specificity on human metaphase 
      chromosomes, resulting in an overall success rate of 94%. Two-color FISH over a 
      479-kb duplication, initially reported as being identical in 2 individuals, 
      revealed distinct 2-color patterns representing direct and inverted duplicons, 
      demonstrating that visualization by high-resolution FISH provides further insight 
      in the fine-scale complexity of genomic structures. The ability to design FISH 
      probes for any sequenced genome along with the ease, reproducibility, and high 
      level of accuracy of this technique suggests that it will be powerful for routine 
      analysis of previously difficult genomic regions and structures.
CI  - Copyright (c) 2010 S. Karger AG, Basel.
FAU - Yamada, N A
AU  - Yamada NA
AD  - Agilent Laboratories, Agilent Technologies, Santa Clara, Calif., USA. 
      alice_yamada@agilent.com
FAU - Rector, L S
AU  - Rector LS
FAU - Tsang, P
AU  - Tsang P
FAU - Carr, E
AU  - Carr E
FAU - Scheffer, A
AU  - Scheffer A
FAU - Sederberg, M C
AU  - Sederberg MC
FAU - Aston, M E
AU  - Aston ME
FAU - Ach, R A
AU  - Ach RA
FAU - Tsalenko, A
AU  - Tsalenko A
FAU - Sampas, N
AU  - Sampas N
FAU - Peter, B
AU  - Peter B
FAU - Bruhn, L
AU  - Bruhn L
FAU - Brothman, A R
AU  - Brothman AR
LA  - eng
PT  - Journal Article
DEP - 20101218
PL  - Switzerland
TA  - Cytogenet Genome Res
JT  - Cytogenetic and genome research
JID - 101142708
SB  - IM
MH  - Chromosome Duplication/*genetics
MH  - Chromosomes, Human/*genetics
MH  - Genome, Human
MH  - Humans
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Male
MH  - Metaphase/genetics
MH  - Oligonucleotide Array Sequence Analysis/methods
MH  - Segmental Duplications, Genomic/genetics
MH  - Sequence Analysis, DNA/methods
MH  - Sequence Inversion
EDAT- 2010/12/24 06:00
MHDA- 2011/04/07 06:00
CRDT- 2010/12/24 06:00
PHST- 2010/09/23 00:00 [accepted]
PHST- 2010/12/24 06:00 [entrez]
PHST- 2010/12/24 06:00 [pubmed]
PHST- 2011/04/07 06:00 [medline]
AID - 000322717 [pii]
AID - 10.1159/000322717 [doi]
PST - ppublish
SO  - Cytogenet Genome Res. 2011;132(4):248-54. doi: 10.1159/000322717. Epub 2010 Dec 
      18.