A Bacterial Artificial Chromosome Library for Sequencing the Complete Human Genome

Osoegawa, Kazutoyo; Mammoser, Aaron; Wu, Cunle; Frengen, Eirik; Zeng, Changjiang; Catanese, Joseph J.; Jong, Pieter J. de

doi:10.1101/gr.169601

Cited by 290 publications

(242 citation statements)

References 52 publications

(54 reference statements)

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“…For the two subjects with atypical deletions negative for the clinical probe, BAC probe RP11-138C22 containing the COMT primer set, was selected for FISH analysis to confirm qPCR results. The BAC originated from the RPCI library 11 of BAC clones (Osoegawa et al 2001), obtained courtesy of the Centre for Applied Genomics at the Hospital for Sick Children (Toronto, Canada). Both ends of the RP11-138C22 clone (AQ383658 and AQ383661) are free of repeats and map with 100% identity only to cytoband 22q11.21 in the interval 18253741-18429812.…”

Section: Fish Studiesmentioning

confidence: 99%

Molecular characterization of deletion breakpoints in adults with 22q11 deletion syndrome

et al. 2006

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22q11 Deletion syndrome (22q11DS) is a common microdeletion syndrome with variable expression, including congenital and later onset conditions such as schizophrenia. Most studies indicate that expression does not appear to be related to length of the deletion but there is limited information on the endpoints of even the common deletion breakpoint regions in adults. We used a real-time quantitative PCR (qPCR) approach to fine map 22q11.2 deletions in 44 adults with 22q11DS, 22 with schizophrenia (SZ; 12 M, 10 F; mean age 35.7 SD 8.0 years) and 22 with no history of psychosis (NP; 8 M, 14 F; mean age 27.1 SD 8.6 years). QPCR data were consistent with clinical FISH results using the TUPLE1 or N25 probes. Two subjects (one SZ, one NP) negative for clinical FISH had atypical 22q11.2 deletions confirmed by FISH using the RP11-138C22 probe. Most (n = 34; 18 SZ, 16 NP) subjects shared a common 3 Mb hemizygous 22q11.2 deletion. However, eight subjects showed breakpoint variability: a more telomeric proximal breakpoint (n = 2), or more centromeric (n = 3) or more telomeric distal breakpoint (n = 3). One NP subject had a proximal nested 1.4 Mb deletion. COMT and TBX1 were deleted in all 44 subjects, and PRODH in 40 subjects (19 SZ, 21 NP). The results delineate proximal and distal breakpoint variants in 22q11DS. Neither deletion extent nor PRODH haploinsufficiency appeared to explain the clinical expression of schizophrenia in the present study. Further studies are needed to elucidate the molecular basis of schizophrenia and clinical heterogeneity in 22q11DS.

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Section: Fish Studiesmentioning

confidence: 99%

Molecular characterization of deletion breakpoints in adults with 22q11 deletion syndrome

et al. 2006

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“…18,19 Detailed protocols are available at the MPI webpage (http://www.molgen.mpg.de/~abt_rop/molecular_ cytogenetics/ProtocolsEntry.html). The patient's DNA and a pooled reference DNA were fluorescently labelled with Cy5 and Cy3, respectively, using the Bioprime Array CGH labelling kit (Invitrogen, Carlsbad, CA, USA).…”

Section: Cytogeneticsmentioning

confidence: 99%

Ulnar–mammary syndrome with dysmorphic facies and mental retardation caused by a novel 1.28 Mb deletion encompassing the TBX3 gene

et al. 2006

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Ulnar -mammary syndrome (UMS) is a rare autosomal-dominant disorder caused by mutations in TBX3. The condition is characterized by hypoplasia or aplasia of upper limbs on the ulnar side, mammary glands and nipples, and of apocrine glands in both sexes (MIM #181450). We report on a girl presenting with an UMS like phenotype, a dysmorphic facies, and mental retardation. Mutation analysis of TBX3 and G-banded chromosome analysis from lymphocytes were performed. We used microarray-based comparative genomic hybridization (array CGH) to investigate the patient's genomic DNA for submicroscopic aberrations. No mutation of the TBX3 gene was detected in our patient and chromosome analysis revealed a normal female karyotype (46,XX). Hybridization of a whole-genome tiling path array consisting of more than 36 000 BAC clones revealed an interstitial 1.28 Mb deletion within chromosomal band 12q24.21. The deleted region encompasses one known gene, TBX3. The deletion and haploinsufficiency of TBX3 was confirmed by fluorescence in situ hybridization using BAC clones representing the deletion on the BAC array. To our knowledge, this is the first description of TBX3 haploinsufficiency caused by a genomic deletion in a patient with UMS. We suggest that the UMS phenotype in conjunction with the characteristic facial changes and mental retardation observed in our patient is owing to the deletion of TBX3 and the involvement of neighbouring genes.

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“…AC010650) and 11-190D6 (GenBank accession no. AC009044) from the RPCI-11 library (Osoegawa et al, 2001) are included in the map based on sequence identity to the probes indicated with dashed lines. Filled circles indicate the T7 end of the PAC clones as determined by the hybridization with Sp6 and T7 oligonucleotides.…”

Section: Expression Of Wwox Mrnas In Human Breast Tumorsmentioning

confidence: 99%

Alternative transcripts of the candidate tumor suppressor gene, WWOX, are expressed at high levels in human breast tumors

et al. 2002

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The presence of putative tumor-suppressor genes on chromosome 16q23.2-24.1 has been suggested by LOH analysis in several cancer types. This region overlaps with the fragile site FRA16D and the region of homozygous deletions found in several cancer types. The candidate gene WWOX/FOR has been mapped within this region. The mouse homologue of the WWOX protein has been de®ned as an apoptogenic protein and an essential partner of p53 in cell death, supporting WWOX as a tumor suppressor gene candidate. We performed an expression study of the WWOX/FOR gene in a series of human breast tumors and breast cancer cell lines, and detected reduced expression of the WWOX/ FOR transcript in a series of breast cancer cells. Furthermore, identi®cation of two distinct alternative WWOX transcripts expressed at high levels in human tumors suggests an involvement of the WWOX gene in breast cancer progression.

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A Bacterial Artificial Chromosome Library for Sequencing the Complete Human Genome

Cited by 290 publications

References 52 publications

Molecular characterization of deletion breakpoints in adults with 22q11 deletion syndrome

Molecular characterization of deletion breakpoints in adults with 22q11 deletion syndrome

Ulnar–mammary syndrome with dysmorphic facies and mental retardation caused by a novel 1.28 Mb deletion encompassing the TBX3 gene

Alternative transcripts of the candidate tumor suppressor gene, WWOX, are expressed at high levels in human breast tumors

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