Searching for genes for cleft lip and/or palate based on breakpoint analysis of a balanced translocation t(9;17)(q32;q12).
OBJECTIVE
Identification of the breakpoints of disease-associated chromosome rearrangements can provide informative clues to a positional cloning approach for genes responsible for inherited diseases. Recently, we found a three-generation Japanese family segregating balanced chromosome translocation t(9;17)(q32;q12). One of the subjects had cleft lip and palate. We examined whether regions near the breakpoint could be associated with cleft lip and/or palate.


METHODS
We determined the breakpoints involved in the translocation by fluorescence in situ hybridization analysis and subsequent long-range polymerase chain reaction. In order to study the role of these disrupted regions in nonsyndromic cleft lip and/or palate, we performed mutation analysis and a haplotype-based transmission disequilibrium test using tagging single-nucleotide polymorphisms in the flanking regions of the breakpoints in white and Filipino nonsyndromic cleft lip and/or palate populations.


RESULTS
Sequence analysis demonstrated that two genes, SLC31A1 (solute carrier family 31 member 1) on chromosome 9 and CCL2 (chemokine ligand 2) on chromosome 17, were rearranged with the breaks occurring within their introns. It is interesting that SLC31A1 lies closed to BSPRY (B-box and SPRY domain), which is a candidate for involvement with cleft lip and/or palate. Some of the variants in BSPRY and CCL2 showed significant p values in the cleft lip and/or palate population compared with the control population. There was also statistically significant evidence of transmission distortion for haplotypes on both chromosomes 9 and 17.


CONCLUSIONS
The data support previous reports that genes on chromosomal regions of 9q and 17q play an important role in facial development.
Machida
Junichiro
J
Department of Maxillofacial Surgery, Aichi-Gakuin University, Nagoya, Japan. jmachida@dpc.aichi-gakuin.ac.jp
Félix
Têmis M
TM
Murray
Jeffrey C
JC
Yoshiura
Koh-ichiro
K
Tanemura
Mitsuyo
M
Kamamoto
Munefumi
M
Shimozato
Kazuo
K
Sonta
Shin-ichi
S
Ono
Takao
T
D027682:Cation Transport Proteins / Q000235:genetics; D018932:Chemokine CCL2 / Q000235:genetics; D019457:Chromosome Breakage; D056905:Chromosome Breakpoints; D002886:Chromosomes, Human, Pair 17 / Q000235:genetics*; D002899:Chromosomes, Human, Pair 9 / Q000235:genetics*; D002971:Cleft Lip / Q000235:genetics*; D002972:Cleft Palate / Q000235:genetics*; D000079923:Copper Transporter 1; D015321:Gene Rearrangement / Q000235:genetics; D006239:Haplotypes; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D007231:Infant, Newborn; D007438:Introns / Q000235:genetics; D008297:Male; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011506:Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA; D014178:Translocation, Genetic / Q000235:genetics*
C416225:BSPRY protein, human; C111835:CCL2 protein, human; D027682:Cation Transport Proteins; D018932:Chemokine CCL2; D000079923:Copper Transporter 1; D011506:Proteins; C490079:SLC31A1 protein, human