Chromosomal assignment of the human SA gene to 16p13.11 and demonstration of its expression in the kidney

The SA gene is a novel gene of yet unknown function recently implicated in blood pressure regulation in rodent models of genetic hypertension. In this study we have located the human homologue of the SA gene to chromosome 16p13.11, by a combination of fluorescence in-situ hybridization and analysis of somatic cell hybrids carrying different segments of chromosome 16. This should facilitate investigation of its role in the genetic tendency to hypertension in humans. Increased expression of the gene in the kidney may be the mechanism through which some allelic variants of the gene raise blood pressure in rodent models. In this study we also demonstrate that the SA gene is expressed in human kidneys.

Isolation and characterization of transcribed sequences from a chromosome 16 hn-cDNA library and the physical mapping of genes and transcribed sequences using a high-resolution somatic cell panel of human chromosome 16

A hn-cDNA (heteronuclear complementary DNA) library was constructed from a mouse/human somatic cell hybrid, CY18, which contains chromosome 16 as the only human chromosome. Hexamer primers constructed from consensus 5' intron splice sequences were used to generate cDNA from the immature unspliced mRNA. The resulting cDNA library was screened with a total human DNA probe to identify potential human clones. Rescreening was necessary, and use of a mouse-derived clone with homology to 7SL RNA proved successful in eliminating the majority of mouse clones. Thirteen clones had open reading frames, and of those, five showed homology to human sequences in GenBank. Two clones had homology to random partially sequenced cDNAs, one clone was likely to be a GRP78 pseudogene, one clone mapped the PHKG2 gene to 16p11.2-16p12.1, and one clone had homology to human S13 ribosomal protein. All clones except the latter were mapped to a high-resolution somatic cell panel. Although isolation of human chromosome 16 genes from this library was successful, it was apparent that cDNA synthesis was initiated at sites other than intron splice sites, presumably by mispairing of the hexamers.

At least two different regions are involved in allelic imbalance on chromosome arm 16q in breast cancer

Loss of heterozygosity (LOH) or allelic imbalance, the latter term referring to both loss and gain of an allele, on the long arm of chromosome 16 has been repeatedly found in cancers of, e.g., the breast and prostate. This indicates the presence of one or more tumor suppressor genes on 16q. To locate the gene(s) more precisely, a detailed allelic imbalance map of 20 polymorphic markers on this chromosome arm was made for 79 sporadic breast carcinomas. LOH of one or more markers was found in 63% of the tumors. Some had allelic imbalance on a region of 16q which failed to overlap with the LOH in other tumors. We therefore assigned two separate "smallest regions of overlap" to 16q and suggest that this chromosome arm contains at least two different tumor suppressor genes.

Allele loss on chromosome 16q24.2-qter occurs frequently in breast cancers irrespectively of differences in phenotype and extent of spread

Loss of heterozygosity on chromosomal arm 16q has been shown to be a frequent event in sporadic breast cancer and is suggested to be involved in cancer development through inactivation of a tumor-suppressor gene. To specify the commonly deleted region in which the unknown tumor-suppressor gene is located, a deletion map of chromosome 16 was constructed for 78 breast cancers, using 27 polymorphic DNA markers. Loss of heterozygosity on chromosome 16q was detected in 38 of the tumors. From the deletion map, the incidence of the loss of heterozygosity was deduced to be > or = 36% in the region distal to 16q12 and was most frequent in the 16q24.2-qter region. Then, association of the loss of heterozygosity in the 16q24.2-qter region with clinicopathological parameters of the tumors was examined for a total of 234 tumors, to reveal its biological significance in breast cancer development. The total incidence of loss of heterozygosity in the 16q24.2-qter region was 52% (118 of 225), and loss of heterozygosity was frequent irrespectively of the presence of invasion and metastasis, differences in clinical stage, tumor size, histological grade, or type, or amounts of estrogen receptor. Inactivation of an unknown tumor-suppressor gene on 16q24.2-qter was thus suggested to be involved commonly in the genesis of sporadic breast cancer, irrespectively of the extent of tumor spread or grade of aggressiveness of the cancer cells. On the other hand, eight cases revealed loss of heterozygosity not at 16q24-qter but in more proximal regions. Therefore, it appears that multiple tumor-suppressor genes are located on chromosome 16q.

Assignment of the human skeletal muscle alpha actin gene (ACTA1) to 1q42 by fluorescence in situ hybridisation

The human skeletal muscle alpha actin gene (ACTA1) has previously been localized to 1p21-->qter using somatic cell hybrids and a specific probe from the 3' untranslated region of the gene. Using fluorescence in situ hybridization the localization has been confirmed and the ACTA1 gene precisely mapped to 1q42.

Identification and regional localization of a human IMP dehydrogenase-like locus (IMPDHL1) at 16p13.13

Sequence-tagged sites (STSs) are versatile chromosomal markers for a variety of genome mapping efforts. In this report, we describe a randomly generated STS (323F4) from human chromosome 16 genomic DNA that has 90.0% sequence identity to the type I human inosine-5'-monophosphate dehydrogenase (IMPDH1) gene and 72% identity to the type II human inosine-5'-monophosphate dehydrogenase (IMPDH2) gene. Additional sequencing by primer walking has provided a total of 1380 bp of the human chromosome 16 sequence. The IMPDH-like sequence 323F4 was regionally localized by PCR analysis of a panel of somatic cell hybrids containing different portions of human chromosome 16 to 16p13.3-13.12, between the breakpoints found in hybrids CY196/CY197 and CY198. This regional mapping assignment was further refined to subband 16p13.13 by high-resolution fluorescence in situ hybridization using cosmid 323F4 as a probe. We conclude that a third, previously undescribed IMPDH locus, termed IMPDHL1, exists at human chromosome 16p13.13.

Association of familial Duane anomaly and urogenital abnormalities with a bisatellited marker derived from chromosome 22

We report a spectrum of defects that were found in an 18-year-old girl who presented for investigation of primary amenorrhea. The patient was found to have Duane anomaly, left renal agenesis, absent uterus, bilateral sensorineural deafness, and bilateral preauricular skin tags and sinuses. Investigation of her family showed that her brother also had Duane anomaly, right renal agenesis, sensorineural deafness, and preauricular skin tags and that their father had preauricular skin tags. Cytogenetic analysis, including in situ hybridisation of peripheral blood lymphocytes, demonstrated a supernumerary bisatellited marker chromosome derived from the region of chromosome 22pter-q11 in the affected individuals. Our findings indicate that a gene or genes located in the region of chromosome 22pter-q11 may be associated with the Duane anomaly and the development of the urogenital tract.

High resolution mapping of interstitial long arm deletions of chromosome 16: relationship to phenotype

The breakpoints of seven interstitial deletions of the long arm of chromosome 16 and two ring chromosomes of this chromosome were mapped by in situ hybridisation or by analysis of mouse/human somatic cell hybrids containing the deleted chromosome 16. Use of a high resolution cytogenetic based physical map of chromosome 16 enabled breakpoints to be assigned to an average resolution of at least 1.6 Mb. In general, interstitial deletions involving q12 or q22.1 have broadly similar phenotypes though there are differences in specific abnormalities. Deletions involving regions more distal, from 16q22.1 to 16q24.1, were associated with relatively mild dysmorphism. One region of the long arm, q24.2 to q24.3, was not involved in any deletion, either in this study or in any previous report. Presumably, monosomy for this region is lethal. In contrast, patients with deletions of 16q21 have a normal phenotype. These results are consistent with the proposed distribution of genes, frequent in telomeric Giesma light band regions but infrequent in G positive bands.

Smooth muscle myosin heavy chain locus (MYH11) maps to 16p13.13-p13.12 and establishes a new region of conserved synteny between human 16p and mouse 16

The human smooth muscle myosin heavy chain locus (MYH11) was mapped by fluorescence in situ hybridization to the middle of the p arm of chromosome 16 using a genomic cosmid clone containing coding sequences of the gene as probe. Probe from coding sequence, when applied to Southern blots of a panel of hybrids containing different portions of human chromosome 16, localized the gene to 16p13.13-13.12. Coding sequence PCR primers, when used on the DNA from a CHO-mouse hybrid clone mapping panel informative for mouse chromosomes, showed that the gene was located on mouse chromosome 16. These results correct a recent assignment of MYH11 from 16q12.2 to the region of the 16p-arm inversion breakpoint seen in acute myelomonocytic leukemia (AMML) M4Eo and demonstrate that the conflicting data do not result from the presence of additional MYH genes on the q arm of the chromosome. Also, a new region of conserved synteny between human 16p and mouse 16 is established.

Identification of an inversion 16 coexisting with an isochromosome 22q by in situ hybridization in a case of childhood AML M4e

Rearrangements involving chromosome 16, including inv(16) (p13q22), del(16)(q22), and t(16;16)(p13;q22), are frequent findings in acute myeloblastic leukemia (AML). Each of these rearrangements can occur as the sole karyotypic change or in association with additional chromosomal abnormalities, including in decreasing order of frequency: trisomy 22, trisomy 8, and deletion of the long arm of chromosome 7. We report a pediatric case of de novo AML, M4e subtype, with a unique combination of inv(16) (p13q22) and i(22q) occurring within the same leukemic clone. The inv(16) was detected by fluorescence in situ hybridization (FISH) analysis with two cosmid probes specific for sequences flanking the inv(16) breakpoint on the long arm of chromosome 16. Use of a chromosome-22-specific painting probe unequivocally identified a small metacentric chromosome as an i(22q). This case illustrates a variation in the association of trisomy 22 with inv(16) and suggests that duplication of the long arm of chromosome 22 may contain critical gene(s) involved in the multistep process of evolution of leukemia with 16q22 abnormalities.

Incidence and origin of "null" alleles in the (AC)n microsatellite markers

Twenty-three (AC)n repeat markers from chromosome 16 were typed in the parents of the 40 CEPH (Centre d'Etude du Polymorphisme Humain) families. Where parents were informative, the entire families were then typed. There were seven markers in which null alleles were demonstrated, as recognized by the apparent noninheritance, by a sib, of a parental allele. Four of these markers showed a null allele in a single sibship, while in the other three at least 30% of the CEPH sibships were shown to have a null allele segregating. One null allele was sequenced and shown to be the result of an 8-bp deletion occurring within the priming sequence for PCR amplification of the (AC)n repeats. In gene mapping or in application to diagnosis, the presence of a segregating null allele will not corrupt the linkage data but could result in loss of information. In isolated instances a segregating null allele may be interpreted as nonpaternity. The presence of a null allele may generate misleading data when individuals are haplotyped to determine the presence of linkage disequilibrium with a disease gene.

Fine genetic mapping of the Batten disease locus (CLN3) by haplotype analysis and demonstration of allelic association with chromosome 16p microsatellite loci

Batten disease, juvenile onset neuronal ceroid lipofuscinosis, is an autosomal recessive neurodegenerative disorder characterized by accumulation of autofluorescent lipopigment in neurons and other cell types. The disease locus (CLN3) has previously been assigned to chromosome 16p. The genetic localization of CLN3 has been refined by analyzing 70 families using a high-resolution map of 15 marker loci encompassing the CLN3 region on 16p. Crossovers in three maternal meioses allowed localization of CLN3 to the interval between D16S297 and D16S57. Within that interval alleles at three highly polymorphic dinucleotide repeat loci (D16S288, D16S298, D16S299) were found to be in strong linkage disequilibrium with CLN3. Analysis of haplotypes suggests that a majority of CLN3 chromosomes have arisen from a single founder mutation.

Physical and genetic mapping of the dipeptidase gene DPEP1 to 16q24.3

We report the subregional physical and genetic mapping on chromosome 16q of a cDNA clone selected as a potential tumor/growth suppressor sequence. By DNA sequencing and RNA expression pattern, this clone was identified as part of the renal dipeptidase gene (DPEP1). Using somatic cell hybrids carrying either different human chromosomes or chromosome 16 segments, we confirm and refine the physical mapping of DPEP1 to the chromosome 16 subregion q24.3. Two RFLPs, a biallelic polymorphism detected by TaqI and a VNTR detected by BamHI, EcoRI, and BglII, are described. Using the VNTR polymorphism, DPEP1 was shown to be linked to D16S7 with a maximum lod score of 5.8 at a recombination fraction of 0.03.

Integration of the cytogenetic and genetic linkage maps of human chromosome 16 using 50 physical intervals and 50 polymorphic loci

A comprehensive genetic linkage map constructed from 50 loci represented by 68 markers was anchored to 50 cytogenetically defined intervals on human chromosome 16. The linear order of the loci on the cytogenetic map was compatible with the independently derived linear order on the genetic map. The sex-averaged genetic length is 164.5 cM, with an average distance between loci of 3.3 cM. Sex-specific distances are 132.8 cM in males and 201.8 cM in females. This is the first detailed synthesis of genetic and cytogenetic maps for any human chromosome and is the first step in correlating the genetic and physical maps of this chromosome. The combined map, containing 15 loci with a minimum heterozygosity of 60% and 6 PCR-formatted microsatellite markers, will be useful for assignment and regional localization of disease genes to this chromosome.

Chromosomal assignment of the uromodulin gene (UMOD) to 16p13.11

We report the chromosomal assignment on chromosome arm 16p of a cDNA clone isolated through its expression in mature kidney and lack of expression in several Wilms tumors. DNA sequencing and analysis of the pattern of RNA expression in different tissues identified this clone as a uromodulin (Tamm-Horsfall glycoprotein, uromucoid; UMOD) sequence. By hybridizing this clone to somatic cell hybrids carrying different human chromosomes or segments of chromosome 16, the gene for UMOD was localized to 16p13.11.

The morquio A syndrome (mucopolysaccharidosis IVA) gene maps to 16q24.3

The gene for N-acetylgalactosamine-6-sulfatase, the deficiency of which results in Morquio A syndrome (mucopolysaccharidosis type IVA), was assigned to chromosome 16 at band q24.3 by fluorescence in situ hybridization. Localization of this band was confirmed by PCR analysis of a somatic cell hybrid panel used for fine mapping of chromosome 16.

Refined physical mapping of chromosome 16-specific low-abundance repetitive DNA sequences

Repetitive DNA sequences have been implicated in the origin of several disease phenotypes, including fragile X syndrome, myotonic dystrophy, and spinal bulbar atrophy. In addition, a complex family of chromosome 16-specific low-abundance repetitive (CH16LAR) DNA sequences have been mapped by fluorescence in situ hybridization to regions of chromosome 16 that undergo breakage/rearrangement in acute nonlymphocytic leukemia (ANLL) cells. It has been hypothesized that these repetitive sequences are causally related to the chromosome rearrangements found in ANLL. Here, we further refine the mapping of CH16LAR sequences with respect to the ANLL inversion breakpoints, using a panel of somatic cell hybrids containing 51 different chromosome 16 breakpoints. These studies indicate that CH16LAR sequences at 16p13 are in close proximity to the ANLL short-arm breakpoint region. However, the region containing the highest density of CH16LAR sequences on the long arm appears to be distal to the region where the ANLL long-arm breakpoint has been mapped. These studies further show that CH16LAR sequences map in close proximity to FRA16D and FRA16A.