PMID- 11381034
OWN - NLM
STAT- MEDLINE
DCOM- 20010920
LR  - 20240321
IS  - 1088-9051 (Print)
IS  - 1088-9051 (Linking)
VI  - 11
IP  - 6
DP  - 2001 Jun
TI  - Sequence-based design of single-copy genomic DNA probes for fluorescence in situ 
      hybridization.
PG  - 1086-94
AB  - Chromosomal rearrangements are frequently monitored by fluorescence in situ 
      hybridization (FISH) using large, recombinant DNA probes consisting of contiguous 
      genomic intervals that are often distant from disease loci. We developed smaller, 
      targeted, single-copy probes directly from the human genome sequence. These 
      single-copy FISH (scFISH) probes were designed by computational sequence analysis 
      of approximately 100-kb genomic sequences. ScFISH probes are produced by long 
      PCR, then purified, labeled, and hybridized individually or in combination to 
      human chromosomes. Preannealing or blocking with unlabeled, repetitive DNA is 
      unnecessary, as scFISH probes lack repetitive DNA sequences. The hybridization 
      results are analogous to conventional FISH, except that shorter probes can be 
      readily visualized. Combinations of probes from the same region gave single 
      hybridization signals on metaphase chromosomes. ScFISH probes are produced 
      directly from genomic DNA, and thus more quickly than by recombinant DNA 
      techniques. We developed single-copy probes for three chromosomal regions-the 
      CDC2L1 (chromosome 1p36), MAGEL2 (chromosome 15q11.2), and HIRA (chromosome 
      22q11.2) genes-and show their utility for FISH. The smallest probe tested was 
      2290 bp in length. To assess the potential utility of scFISH for high-resolution 
      analysis, we determined chromosomal distributions of such probes. Single-copy 
      intervals of this length or greater are separated by an average of 29.2 and 22.3 
      kb on chromosomes 21 and 22, respectively. This indicates that abnormalities seen 
      on metaphase chromosomes could be characterized with scFISH probes at a 
      resolution greater than previously possible.
FAU - Rogan, P K
AU  - Rogan PK
AD  - Section of Medical Genetics and Molecular Medicine, Children's Mercy Hospital and 
      Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, 
      Missouri 64108, USA. progan@cmh.edu
FAU - Cazcarro, P M
AU  - Cazcarro PM
FAU - Knoll, J H
AU  - Knoll JH
LA  - eng
PT  - Comparative Study
PT  - Journal Article
PL  - United States
TA  - Genome Res
JT  - Genome research
JID - 9518021
RN  - 0 (DNA Probes)
SB  - IM
MH  - *Base Sequence
MH  - Chromosomes, Human, Pair 21/genetics
MH  - Chromosomes, Human, Pair 22/genetics
MH  - DNA Probes/analysis/*chemical synthesis/isolation & purification
MH  - Gene Dosage
MH  - Genome, Human
MH  - Humans
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Nucleic Acid Hybridization
MH  - Research Design
MH  - Sequence Analysis, DNA/*methods
PMC - PMC311125
EDAT- 2001/05/31 10:00
MHDA- 2001/09/21 10:01
PMCR- 2001/12/01
CRDT- 2001/05/31 10:00
PHST- 2001/05/31 10:00 [pubmed]
PHST- 2001/09/21 10:01 [medline]
PHST- 2001/05/31 10:00 [entrez]
PHST- 2001/12/01 00:00 [pmc-release]
AID - GR-1717R [pii]
AID - 10.1101/gr.171701 [doi]
PST - ppublish
SO  - Genome Res. 2001 Jun;11(6):1086-94. doi: 10.1101/gr.171701.