A Sequence-Ready BAC Contig of the GABAA Receptor Gene Cluster Gabrg1–Gabra2–Gabrb1 on Mouse Chromosome 5

The type-A receptors for the neurotransmitter GABA (gamma-aminobutyric acid) are ligand-gated chloride channels that mediate postsynaptic inhibition. The functional diversity of these receptors comes from the use of a large repertoire of subunits encoded by separate genes, as well as from differences in subunit composition of individual receptors. In mammals, a majority of GABA(A) receptor subunit genes are located in gene clusters that may be important for their regulated expression and function. We have established a high-resolution physical map of the cluster of genes encoding GABA(A) receptor subunits alpha2 (Gabra2), beta1 (Gabrb1), and gamma(1) (Gabrg1) on mouse chromosome 5. Rat cDNA probes and specific sequence probes for all three GABA(A) receptor subunit genes have been used to initiate the construction of a sequence-ready contig of bacterial artificial chromosomes (BACs) encompassing this cluster. In the process of contig construction clones from 129/Sv and C57BL/6J BAC libraries were isolated. The assembled 1.3-Mb contig, consisting of 45 BACs, gives five- to sixfold coverage over the gene cluster and provides an average resolution of one marker every 32 kb. A number of BAC insert ends were sequenced, generating 30 new sequence tag sites (STS) in addition to 6 Gabr gene-based and 3 expressed sequence tag (EST)-based markers. STSs from, and surrounding, the Gabrg1-Gabra2-Gabrb1 gene cluster were mapped in the T31 mouse radiation hybrid panel. The integration of the BAC contig with a map of loci ordered by radiation hybrid mapping suggested the most likely genomic orientation of this cluster on mouse chromosome 5: cen-D5Mit151-Gabrg1-Gabra2-Gabrb1-D5Mit58- tel. This established contig will serve as a template for genomic sequencing and for functional analysis of the GABA(A) gene cluster on mouse chromosome 5 and the corresponding region on human chromosome 4.     

8p11.2亚带ANK1位点附近区域YAC连续克隆群的构建

我们分离了３个８ｐ１１．２亚带ＡＮ中位点附近区域的单拷贝片段，应用这些片段之一Ｓ９２５作为探针筛到４个阳性ＣＥＰＨＹＡＣ克隆结合文献报道资料及其多态性位标检测结果。我们在ＡＮＫ１附近区域构建一个ＹＡＣ连续克隆群，从而填补了Ｄ８Ｓ５３２和Ｄ８Ｓ２６８之间的间隙。这个ＹＡＣ连续克隆群要用于分离基因，为筛选定位在这个区域的致病基因提供候选基因。     

Integrated YAC Contig Map of the Prader–Willi/Angelman Region on Chromosome 15q11–q13 with Average STS Spacing of 35 kb

Prader–Willi syndrome and Angelman syndrome are associated with parent-of-origin-specific abnormalities of chromosome 15q11–q13, most frequently a deletion of an ~4-Mb region. Because of genomic imprinting, paternal deficiency of this region leads to PWS and maternal deficiency to AS. Additionally, this region is frequently involved in other chromosomal rearrangements including duplications, triplications, or supernumerary marker formation. A detailed physical map of this region is important for elucidating the genes and mechanisms involved in genomic imprinting, as well as for understanding the mechanism of recurrent chromosomal rearrangments. An initial YAC contig extended from D15S18 to D15S12 and was comprised of 23 YACs and 21 STSs providing an average resolution of about one STS per 200 kb. To close two gaps in this contig, YAC screening was performed using two STSs that flank the gap between D15S18 and 254B5R and three STSs located distal to the GABRA5–149A9L gap. Additionally, we developed 11 new STSs, including seven polymorphic markers. Although several groups have developed whole-genome genetic and radiation hybrid maps, the depth of coverage for 15q11–q13 has been somewhat limited and discrepancies in marker order exist between the maps. To resolve the inconsistencies and to provide a more detailed map order of STSs in this region, we have constructed an integrated YAC STS-based physical map of chromosome 15q11–q13 containing 118 YACs and 118 STSs, including 38 STRs and 49 genes/ESTs. Using an estimate of 4 Mb for the size of this region, the map provides an average STS spacing of 35 kb. This map provides a valuable resource for identification of disease genes localized to this region as well as a framework for complete DNA sequencing.     

A 3-Mb High-Resolution BAC/PAC Contig of 12q22 Encompassing the 830-kb Consensus Minimal Deletion in Male Germ Cell Tumors

Cytogenetic and molecular genetic analyses have shown that the 12q22 region is recurrently deleted in male germ cell tumors (GCTs), suggesting that this site may harbor a tumor suppressor gene (TSG). Previous loss of heterozygosity (LOH) analyses identified a consensus minimal deleted region between the markers D12S377 and D12S296, and a YAC clone contig covering the region was generated. Here, we describe a high-resolution sequence-ready physical map of this contig covering a 3-Mb region. The map comprised of 52 cosmids, 49 PACs, and 168 BACs that were anchored to the previous YAC contig; 99 polymorphic, nonpolymorphic, EST, and gene-based markers are now placed on this map in a unique order. Of these, 61 markers were isolated in the present study, including one that was polymorphic. In addition, we have narrowed the minimal deletion to approximately 830 kb between D12S1716 (proximal) and P382A8-AG (distal) by LOH analysis of 108 normal-tumor DNAs from GCT patients using 21 polymorphic STSs. These physical and deletion maps should prove useful for identification of the candidate TSG in GCTs, provide framework to generate complete DNA sequence, and ultimately generate a gene map of this segment of the chromosome 12. [The sequence data described in this paper have been submitted to the Genome Survey Sequence under accession nos. AQ254896-AQ254955 and AQ269251-AQ269266. Online supplementary material is available at http://www.genome.org]     

M-banding characterization of a 16p11.2p13.1 tandem duplication in a child with autism, neurodevelopmental delay and dysmorphism

We describe a partial duplication of the chromosome 16 short arm [46,XY,dup(16)(p11.2p13.1)] in an Iranian girl with autism, neurodevelopmental delay, mental retardation, very poor memory, and dysmorphism including sparse hair, upslanting palpebral fissures, long philtrum, micrognathia, hypotonia, small feet and hands, syndactyly of the fingers, and hypoplastic thumbs. The patient now four years old, has a normal twin sister, and the parents are unrelated. The abnormal 16p was originally detected by banding cytogenetic techniques, and was characterized by multicolour banding fluorescence in situ hybridization (MCB). The MCB pattern on the derivative chromosome 16 indicated a direct duplication of the region 16p11.2 to 16p13.1.     

De novo trisomy 16p11.2‐qter: Report of an infant

We report on a four‐month‐old girl with a de novo trisomy 16q [47,XX,+del(16)(p11.2).ish del(16)(p11.2)(wcp16+,D16Z2+,tel16q+, tel16p−)]. She had minor facial anomalies, limb anomalies, urogenital abnormalities, and severe cardiovascular defects. Autopsy confirmed left hypoplastic lung, total anomalous pulmonary venous drainage via coronary sinus, persistent left superior vena cava, patent ductus arteriosus, secundum atrial septal defect, bilateral hydronephrosis and hydroureters, uterus bicornis, and ovarian hypoplasia. Short tandem repeat polymorphism analysis indicated that the additional, structurally abnormal chromosome 16 was maternal in origin. Am. J. Med. Genet. 92:308–310, 2000. © 2000 Wiley‐Liss, Inc.     

Chromosome 10p11.2‐p12.2 duplication: Report of a patient and review of the literature

We report on a young male with mental retardation, slightly upslanting palpebral fissures, strabismus, high‐arched palate, retrognathia, and flat feet. Cytogenetic analysis in addition to fluorescent in situ hybridization (FISH) and comparative genomic hybridization (CGH) showed the presence of a chromosome 10p11.2→p12.2 duplication. Karyotypes of the parents were normal. Comparison of the clinical findings observed in the present patient with those observed in other reported cases with duplication 10p suggest that the presence of high arched/cleft palate and retrognathia may be related to the 10p11.2→p12.2 duplication. Also, no critical region for the trisomy 10p syndrome has been delimited. © 2001 Wiley‐Liss, Inc.     

Localization of the chromosomal breakpoints of the t(12;16) in liposarcoma to subbands 12q13.3 and 16p11.2

Short-term cultures of two myxoid liposarcomas and two mixed-type (myxoid and round cell) liposarcomas were cytogenetically analyzed. A t(12;16)(q13;p11) was present in three tumors, whereas the fourth had an unbalanced 12;16-translocation with breaks in 12q13 and 12q22, with loss of the 12q13-q22 segment, and in 16p11. In the two mixed liposarcomas, the breakpoints could be determined at subband level to 12q13.3 and 16p11.2.     

Complete trisomy 17p syndrome in a girl with der(14)t(14;17)(p11.2;p11.2)

We report on an 8-year-old girl with near-complete trisomy 17p syndrome due to a de novo unbalanced t(14;17)(p11.2;p11.2). She has features consistent with the previously described cases with complete trisomy 17p, including pre- and post-natal growth retardation, motor and mental retardation, skeletal anomalies, clinodactyly of the 5th finger, hypertrichosis, as well as facial characteristics including microcephaly, receding forehead, ptosis, low-set malformed ears, smooth philtrum, high-arched palate, and a short broad neck. Fluorescence in situ hybridization showed that the breakpoints were p11.2 for both chromosome 14 and 17. Microsatellite analysis showed that the duplicated 17p was of paternal origin, and indicated that the breakpoint involving 17p11.2 is most likely located within the approximately 1-Mb segment from the centromere, and not involving the proximal Smith-Magenis syndrome (SMS) low copy repeat. We compare the clinical features of our patient with those previously reported to further delineate the phenotype of complete trisomy 17p syndrome.     

Duplication of chromosome region (16)(p11.2 → p12.1) in a mother and daughter with mild mental retardation

We report a 40‐year‐old female with mild mental retardation and behavior problems and her 6‐year‐old daughter. Chromosome analysis showed that both patients had a proximal duplication in the short arm of chromosome 16. The aberration was characterized further with band‐specific probes, resulting in a 46,XX,dir dup(16)(pter → p11.2::p12.1 → qter) karyotype. The clinical and cytogenetical findings are compared to other patients with partial trisomy 16p reported in the literature. © 2002 Wiley‐Liss, Inc.     

Pseudodicentric (16;12)(q11;p11.2) in a type AB (mixed) thymoma.

Genetic alterations of thymomas are rarely described in the literature. In this study, a previously unreported instance of aberrant karyotypic change consisting of 45,XX,pseu dic(16;12) (q11;p11.2) [cp23]/87-90,idemx2[cp4] in a Masaoka Stage II mixed thymoma or type AB thymoma affecting a 56-year-old Chinese woman is detailed. Abnormalities involving 12p containing important tumor suppressor-like genes have been documented especially in hematological malignancies. Recently, recurrent losses involving 16q, a locus known to harbor several tumor suppressor genes, have been described in type C thymomas (squamous cell carcinoma), suggesting a possible relationship between type AB thymoma and type C thymoma. Whether these genes are involved in the pathogenesis of type AB thymoma remain to be clarified and it is currently unclear if cytogenetic studies may eventually play a role in the classification of thymic tumors.     

A Matrix Associated Region Localizes the Human SOCS-1 Gene to Chromosome 16p13.13

The MarFinder algorithm was applied to a newly sequenced segment of 16p13.13 abutting the 3 end of the human PRM1 PRM2 TNP2 locus. A candidate region of matrix attached was identified. Subsequent biophysical analysis showed that this region was attached to the somatic nuclear matrix. Nucleotide sequence analysis also revealed the presence of a CpG island. Data base queries showed that this region contained the SOCS-1 gene. Thus, the SOCS-1 gene is bounded by a somatic MAR and is just 3 of the spermatid-expressed PRM1 PRM2 TNP2 domain at position 16p13.13.     

A large interstitial deletion of 17p13.1p11.2 involving the Smith-Magenis chromosome region in a girl with multiple congenital anomalies

A 6-month-old girl had multiple congenital anomalies, including dysmorphic face; tetralogy of Fallot, pulmonary atresia and patent ductus arteriosus; congenital cystic adenomatoid malformation of the right upper lung, and hemilateral kidney defect. Chromosome analysis as well as fluorescence in situ hybridization (FISH) and polymorphic marker analyses in the girl and her parents revealed a de novo large interstitial deletion of 17p13.1-p11.2 of the paternally derived chromosome 17. The deletion involved the Smith-Magenis chromosome region (SMCR). Lack of involvement of the Miller-Dieker syndrome region at 17p13.3 was confirmed by both FISH analysis and radiological examinations that showed no migrational abnormality. The girl died at age 7 months. This is the first report of a patient with a large interstitial deletion of 17p.     

A new nonrandom chromosomal abnormality, t(2;16)(p11.2;p11.2), possibly associated with poor outcome in childhood acute lymphoblastic leukemia.

We report a new, nonrandom t(2;16)(p11.2;p11.2) in childhood acute lymphoblastic leukemia (ALL). Three of 292 patients with childhood ALL studied at Indiana University Medical Center had this translocation. All three had additional chromosomal abnormalities at diagnosis and were classified as having low hyperdiploidy (47-49 chromosomes) with structural abnormalities. The patients, two boys and one girl, ranged in age from 3 to 13 years. Peripheral white blood cells (WBC) counts ranged from 1.8 to 107.4 x 10(9)/L, all were classified as French-American-British (FAB) type L1, and all had B-lineage ALL. Because all three patients have relapsed after first remissions of 2 years 8 months to 6 years, the t(2;16) may indicate a poor prognosis and more aggressive treatment may be indicated for such patients. Because this translocation was the sole abnormality in one clone of patient 2 at relapse, it may be considered the primary abnormality. Therefore, it may also be the primary abnormality in the other two patients, and the genes involved in the breakpoints may be important in leukemogenesis.