Exclusion gene mapping utilizing patients with chromosome imbalance: The HL-A system as a prototype

Summary 17 chromosomally unbalanced patients, their siblings and parents were tested for HL-A types and for up to 25 other polymorphic systems to determine whether there was gain or loss of an allele concurrent with the gain or loss of chromosome material. 5 patients had trisomy of part or all of a chromosome; 2 had trisomy of a segment and also deletion of chromosome material. All 7 were due to a familial translocation. The remaining patients had small deletions; 5 had ring chromosomes, 4 had rod deletions and 1 had missing chromosome material due to a heritable translocation. All cases were informative at the HL-A loci because of the high degree of polymorphism of the system whereas only some of the other systems were informative. None of the 17 patients showed unusual inheritance of HL-A or any other of the polymorphic systems examined. These results provide evidence excluding the HL-A and other loci from a number of possible locations in the human genome.Supported by Maternal and Child Health Services 920 and a grant from the Medical Research Foundation of Oregon.Supported by NIH grants AM 13173 and HD-05082 and a Basil O'Connor Starter Research Grant from the National Foundation March of Dimes.Supported by Crippled Children's Division of Oregon Summer Student Funds.Supported by a grant from the National Foundation March of Dimes.     

Deletions in human chromosome arms 11p and 13q in primary hepatocellular carcinomas

Normal liver and hepatocellular carcinoma (HCC) genotypes were compared at loci on most of the human chromosomes with probes that detect restriction fragment length polymorphisms. Six of fourteen tumors exhibited loss of heterozygosity of one or more markers on 11p. Ten patients were informative for loci on 13q, and 5 of these 10 exhibited loss of heterozygosity for one or more of the 13q markers. Altogether, 9 of the 14 patients showed loss of a polymorphic allele for one or more loci on either 11p or 13q. A survey of loci on 16 additional chromosomes indicated that the deletions were not due to a general loss of heterozygosity in HCCs. Quantitative densitometry showed that each of the 10 deletions resulted in hemizygosity (no reduplication) of the remaining allele in tumor tissue. In contrast to hereditary embryonal tumors, in which reduplication of the remaining chromosome is the rule, simple deletion appears to be the primary mechanism responsible for the loss of heterozygosity in these adult, nonhereditary HCCs. These data show that HCCs arising in hepatitis B virus carriers are a genetically heterogeneous group of tumors, some of which may arise through 13q alterations, some through 11p alterations, some with both chromosomes altered, and some with both intact.     

Refined physical and genetic mapping of the NF1 region on chromosome 17.

A total of 15 polymorphic markers were used to construct a genetic map that encompasses the NF1 locus on chromosome 17. The markers were a subset of a large collection of chromosome 17-specific probes and were selected for marker typing in NF1 families after physical localization to the pericentric region of the chromosome. Multilocus data for a total of 17 informative NF1 families and 39 other families were included in genetic analyses. No recombination was observed between NF1 and four markers, one or more of which was informative in 86% of parents. More-refined physical mapping studies demonstrated that all four of the markers are proximal to the chromosome 17 translocation breakpoints from two NF1 patients bearing balanced translocations. The region flanking the disease locus spans a distance of 1 centimorgan (cM) in males and 9 cM in females. Close flanking markers were informative in 76% of meioses. Sex differences in recombination rates in the pericentric region were highly significant statistically.     

Allelotyping of human prostatic adenocarcinoma.

Allelotyping (using at least one probe detecting a restriction fragment length polymorphism on each chromosomal arm, with the exception of the short arms of the acrocentric chromosomes), showed loss of genetic information in 11 of 18 prostate adenocarcinoma specimens analyzed (61%). Frequent allelic deletions were detected on the long arm of chromosome 16 (6 of 10 informative cases, 60%), on the short arm of chromosome 8 (3 of 6 informative cases, 50%), and on the short and/or the long arms of chromosome 10 (6 of 11 informative cases (10p), 55% and 4 of 13 informative cases (10q), 30%, respectively). No losses of alleles were detected in any case unless at least one of the chromosomes 8, 10, or 16 also showed deletions. The long arm of chromosome 18 also showed a high frequency of allelic deletions (3 of 7 informative cases, 43%). Allelic deletions on the following chromosomes were detected at lower frequencies: chromosomes 2, 3, 7, 12, 13, 17, 22, and XY. Tumors with allelic deletions on more than one chromosome had a higher histological malignancy grade. Tumors from patients with advanced disease all showed allelic deletions.     

Characterization of newly established colorectal cancer cell lines: correlation between cytogenetic abnormalities and allelic deletions associated with multistep tumorigenesis

We have established a series of 20 colorectal cancer cell lines and performed cytogenetic and RFLP analyses to show that the recurrent genetic abnormalities of chromosomes 1, 5, 17 and 18 associated with multistep tumorigenesis in colorectal cancer, and frequently detected as recurrent abnormalities in primary tumours, are also retained in long-term established cell lines. Earlier studies by us and other investigators showed that allelic losses of chromosomes 1 and 17 in primary colorectal cancers predicted poorer survival for the patients (P = 0.03). We utilized the cell lines to identify specific chromosomal sites or gene(s) on chromosomes 1 and 17 which confer more aggressive phenotype. Cytogenetic deletions of chromosome 1p were detected in 14 out of the 20 (70%) cell lines, whereas allelic deletions for 1p using polymorphic markers were detected in 13 out of 18 (72%) informative cell lines for at least one polymorphic marker. We have performed Northern blotting, immunohistochemical staining (p53 mRNA, protein) and RFLP analysis using several probes including p53 and nm23. RFLP analysis using a total of seven polymorphic markers located on 17p and 17q arms showed allelic losses aroundthe p53 locus in 16 out of the 20 cell lines (80%), four of which were losses of thep53 locus itself. In addition, seven cell lines (out of nine informative cases) also showed losses of thenm23 gene, four with concurrent losses of thep53 locus, while the remaining three were homozygous. In addition, five out of seven cell lines withnm23 deletions were derived from hepatic metastatic tumours, and one cell line was obtained from recurrent tumour. A comparison between allelic deletions of 1p and functional loss ofnm23 gene revealed a close association between these two events in cell lines derived from hepatic metastasis. Following immunohistochemical staining, nine out of the twenty cell lines showed high levels (25–80%) of mutant p53, four showed intermediate levels (>20%), and seven had undetectable levels of the protein. Of these seven, four showed complete absence of mRNA. Of the remaining three cell lines one showed aberrant mRNA due to germline rearrangement of thep53 gene, whereas in two cell lines normal levels of mRNA were present. Nineteen of the 20 cell lines had normal germline configurations for thep53 gene, while one showed a rearrangement. These data suggest that functional loss ofp53 andnm23 genes accomplished by a variety of mechanisms may be associated with poor prognosis and survival. In addition, concurrent deletions of chromosome regions 17p, 17q and 1p were closely associated with high-stage hepatic metastatic disease. These cell lines with well-characterized genetic alterations and known clinical history provide an invaluable source of material for various biological and clinical studies relating to multistep colorectal tumorigenesis.     

The frequency of aneuploidy in cultured lymphocytes is correlated with age and gender but not with reproductive history.

The clinical significance of low numbers of aneuploid cells in routine cytogenetic studies of cultured lymphocytes is not always clear. We compared the frequencies of chromosome loss and gain among five groups of subjects whose karyotypes were otherwise normal; these groups were (1) subjects studied because of multiple miscarriages, (2) parents of live borns with autosomal trisomy, (3) subjects studied because they had a relative with Down syndrome, (4) an age-matched control group of phenotypically normal adults studied for other reasons (e.g., parent of a dysmorphic child or member of a translocation family), and (5) other mostly younger and phenotypically abnormal subjects who could not be assigned to the first four groups (e.g., individuals with multiple congenital anomalies or mental retardation). No significant age, sex, or group effects were observed for autosomal loss (hypodiploidy) or gain (hyperdiploidy). Autosomal loss was inversely correlated with relative chromosome length, but autosomal gain was not. Sex-chromosome gain was significantly more frequent in females than in males, but sex-chromosome loss was not significantly different between the sexes. Significant age effects were observed for both gain and loss of sex chromosomes. When age and sex were accounted for, the frequencies of sex-chromosome loss and gain were not significantly different among the five clinical groups. In general, low numbers of aneuploid cells are not clinically important when observed in blood chromosome preparations of subjects studied because of multiple miscarriages or a family history of autosomal trisomy.     

Allelotype of human thyroid tumors: loss of chromosome 11q13 sequences in follicular neoplasms.

Two classes of genes are the targets of mutations involved in human tumorigenesis: oncogenes, the activation of which leads to growth stimulation, and tumor suppressor genes, which become tumorigenic through loss of function, often through allelic deletion. To obtain evidence for a role for tumor suppressor genes in thyroid tumorigenesis, we examined DNA from 80 thyroid neoplasms for loss of heterozygosity in multiple chromosomal loci using 19 polymorphic genomic probes. None of the informative thyroid tumors studied had allelic loss detected with probes for chromosome 2q (D2S44), 3p (D3F15S2, D3S32), 3q (D3S46), 4p (D4S125), 6p (D6S40), 8q (D8S39), 9q (D9S7), 12p (D12S14), 13q (D13S52), 17p (D17S30), or 18q (D18S10). One of eight of the follicular adenomas had a 10q deletion detected with marker D10S15, and one of 26 had a 10q deletion detected with D10S25. One of two of the follicular carcinomas had an 11p deletion in the H-ras locus. The most significant findings were on chromosome 11q13, the site containing the putative gene predisposing to multiple endocrine neoplasia type I. Four of 27 follicular adenomas had loss of heterozygosity for probes in this region. Allelic deletions were detected with the following probes: D11S149, PYGM, D11S146, and INT2. None of 13 informative papillary carcinomas and none of two follicular carcinomas had loss of heterozygosity detectable with these 11q13 markers. Allelic loss is a relatively infrequent event in human thyroid tumors. Deletions of chromosome 11q13 are present in about 14% of follicular, but not papillary, neoplasms.(ABSTRACT TRUNCATED AT 250 WORDS)     

Familial trisomy 20p five cases and two carriers in three generations a review.

A clinically normal mother of three retarded children has been determined by G-banding to have a balanced translocation 46,XX,t(13;20) (q34;p11.2). The children each have an unbalanced form of the translocation with partial trisomy for 20p. Extensive gene marker studies have been unable to affix any specific gene locus onto the short arm of chromosome 20. The balanced translocation was inherited from the maternal grandfather. Two phenotypically abnormal deceased members of the family are believed to have had the unbalanced trisomy 20p condition. An increases number of spontaneous abortions were possibly due to lethal unbalanced 20p deletions. The moderate to mild mental retardation and somewhate unusual features (round face, prominent cheeks and nose, short mandible) in the three siblings and two other affected relatives suggest that trisomy of the short arm of chromosome 20 may cause a distinguishable clinical syndrome. Vertebral abnormalities and abnormal dermatoglyphics are part of the picture. Clinical and cytogenetic findings of all reported cases are compared.     

Two independent chromosomal rearrangements, a very small (550 kb) duplication of the 7q subtelomeric region and an atypical 17q11.2 (NF1) microdeletion, in a girl with neurofibromatosis

Most patients with neurofibromatosis (NF1) are endowed with heterozygous mutations in the NF1 gene. Approximately 5% show an interstitial deletion of chromosome 17q11.2 (including NF1) and in most cases also a more severe phenotype. Here we report on a 7-year-old girl with classical NF1 signs, and in addition mild overgrowth (97th percentile), relatively low OFC (10th-25th percentile), facial dysmorphy, hoarse voice, and developmental delay. FISH analysis revealed a 17q11.2 microdeletion as well as an unbalanced 7p;13q translocation leading to trisomy of the 7q36.3 subtelomeric region. The patient's mother and grandmother who were phenotypically normal carried the same unbalanced translocation. The 17q11.2 microdeletion had arisen de novo. Array comparative genomic hybridization (CGH) demonstrated gain of a 550-kb segment from 7qter and loss of 2.5 Mb from 17q11.2 (an atypical NF1 microdeletion). We conclude that the patient's phenotype is caused by the atypical NF1 deletion, whereas 7q36.3 trisomy represents a subtelomeric copy number variation without phenotypic consequences. To our knowledge this is the first report that a duplication of the subtelomeric region of chromosome 7q containing functional genes (FAM62B, WDR60, and VIPR2) can be tolerated without phenotypic consequences. The 17q11.2 microdeletion (containing nine more genes than the common NF1 microdeletions) and the 7qter duplication were not accompanied by unexpected clinical features. Most likely the 7qter trisomy and the 17q11.2 microdeletion coincide by chance in our patient.     

An unusually proximal deletion on the short arm of chromosome 3 in a patient with small cell lung cancer.

The tumors of patients with small cell lung carcinoma (SCLC) frequently exhibit the loss of alleles at polymorphic loci on the short arm of chromosome 3. We report the genotype analysis of six SCLC patients obtained using 15 chromosome 3 probes that identified 19 restriction fragment length polymorphisms (RFLPs). Five of the six patients were reduced to homozygosity in the tumor DNA at every informative 3p locus, and thus did not serve to delineate the deletion. However, the RFLP analysis of the tumor DNA of the sixth patient demonstrated both heterozygous and hemizygous loci on 3p and allowed the definition of an interstitial deletion that extends proximal to the D3S2 locus at 3p14.2-p21 to include at least 3p13-p14. The exclusion of the D3F15S2 locus from the deleted region, observed in this patient, is an uncharacteristic feature of SCLC deletions. This deletion includes the location of D3S30 and D3S4, and thus serves to map these loci within the proximal half of chromosome 3.     

Linkage group HL-A-MLC-BF (properdin factor B). The site of the Bf locus at the immunogenetic linkage group on chromosome 6.

Genetic linkage between the HL-A and Bf loci could be confirmed in 43 families with 168 offspring. In 4 families, 5 recombinants out of 82 informative meiotic divisions were observed (r = 6.1%). The localisation of the Bf marker system was studied in 3 families with crossovers between HL-A and MLC. From these data the following map order of human chromosome 6 can be proposed: HL-A (1st locus) -- HL-A (2nd locus)--MLC-Bf---PGM(3). The fact that important components of the classical and alternate pathway of complement activation are governed by genes closely linked with HL-A and MLC loci leads to the proposition to include the Bf system into the Major Histocompatibility Complex in man.     

Non-reciprocal chromosomal bridge-induced translocation (BIT) by targeted DNA integration in yeast

Several experimental in vivo systems exist that generate reciprocal translocations between engineered chromosomal loci of yeast or Drosophila, but not without previous genome modifications. Here we report the successful induction of chromosome translocations in unmodified yeast cells via targeted DNA integration of the KAN^R selectable marker flanked by sequences homologous to two chromosomal loci randomly chosen on the genome. Using this bridge-induced translocation system, 2% of the integrants showed targeted translocations between chromosomes V-VIII and VIII-XV in two wild-type Saccharomyces cerevisiae strains. All the translocation events studied were found to be non-reciprocal and the fate of their chromosomal fragments that were not included in the translocated chromosome was followed. The recovery of discrete-sized fragments suggested multiple pathway repair of their free DNA ends. We propose that centromere-distal chromosome fragments may be processed by a break-induced replication mechanism ensuing in partial trisomy. The experimental feasibility of inducing chromosomal translocations between any two desired genetic loci in a eukaryotic model system will be instrumental in elucidating the molecular mechanism underlying genome rearrangements generated by DNA integration and the gross chromosomal rearrangements characteristic of many types of cancer.Electronic Supplementary Material Supplementary material is available for this article at     

Two sibs with duplication of 4q31-->qter due to 3:1 meiotic disjunction and mild phenotype

Two sibs with duplication of 4q31-->qter due to 3:1 meiotic disjunction and mild phenotype: Clinical and cytogenetic findings in two sibs with partial duplication of 4q31.3-->qter and 21q11.2-->pter are reported. These patients are rare cases of reoccurrence of those partial trisomies due to 3:1 segregation of a maternal balanced translocation. A review of the literature reporting cases of trisomy of the 4q31-->qter segment is also made; previously reported cases mostly in addition have deletions of other chromosomes resulting from adjacent segregation of balanced translocation. The findings of our study confirm the high risk for offspring with unbalanced rearrangements in women with reciprocal translocation involving acrocentric and short chromosome segments. The study also points out that duplication of 4q31-->qter may go along with only mild phenotypic findings if there is no significant additional aneuploidy of the other chromosome involved in the rearrangement.     

Retained heterodisomy for chromosome 12 in atypical lipomatous tumors: implications for ring chromosome formation

Atypical lipomatous tumor (ALT) is an intermediate malignant mesenchymal tumor that is characterized by supernumerary ring chromosomes and/or giant rod-shaped marker chromosomes (RGMC). Fluorescence in situ hybridization (FISH) and molecular genetic analyses have disclosed that the RGMCs always contain amplified sequences from the long arm of chromosome 12. Typically, RGMCs are the sole clonal changes and so far no deletions or other morphologic aberrations of the two normal-appearing chromosomes 12 that invariably are present have been detected. The mechanisms behind the formation of the RGMCs are unknown, but it could be hypothesized that RGMC formation is preceded by trisomy 12 or, alternatively, that ring formation of one chromosome 12 is followed by duplication of the remaining homolog. The latter scenario would always result in isodisomy for the two normal-appearing chromosomes 12, whereas the former would yield isodisomy in one-third of the cases. In order to investigate these possible mechanisms behind ring formation, we studied polymorphic loci on chromosome 12 in 14 cases of ALT showing one or more supernumerary ring chromosomes and few or no other clonal aberrations at cytogenetic analysis. The molecular genetic analyses showed that the tumor cells always retained both parental copies of chromosome 12, thus refuting the trisomy 12 and duplication hypotheses.     

Loss of 3p or 11p alleles is associated with testicular cancer tumors

Constitutional and tumor genotypes defined by polymorphic DNA markers were examined in 31 testicular cancer patients. Constitutional karyotypes were analyzed and clinical data presented. We analyzed 11 loci representing 8 chromosomes, including regions frequently deleted in other types of cancer. Loss of 3p or 11p sequences was detected in 8 of 28 heterozygotes (28%) and in 5 of 20 heterozygotes (25%). This gives a combined total loss of 40%. The other autosomal loci tested showed no loss or a loss of less than 10% of alleles. We suggest that this loss of heterozygosity for genetic material on chromosome 3p or on 11p is nonrandom and important in the development of a major subset of testicular neoplasms.     

A case with laryngeal atresia and partial trisomy 9 due to maternal 9;16 translocation.

A newborn with a partial trisomy 9 and a partial trisomy 16q is described. The child died shortly after birth because of laryngeal atresia. The chromosome anomaly was the result of a 3:1 segregation of a maternal translocation t(9;16) (q22;q24). The pertinent literature on both partial trisomy 9 and partial trisomy 16q is reviewed. All cases with partial trisomy 9 were either de novo or the result of a maternal translocation, possibly indicating the influence of imprinting on this chromosomal abnormality. The relationship between the laryngeal atresia and other features in the patient and the chromosome anomalies remains uncertain.     

Clinical and molecular diagnosis of Miller-Dieker syndrome.

We report results of clinical, cytogenetic, and molecular studies in 27 patients with Miller-Dieker syndrome (MDS) from 25 families. All had severe type I lissencephaly with grossly normal cerebellum and a distinctive facial appearance consisting of prominent forehead, bitemporal hollowing, short nose with upturned nares, protuberant upper lip, thin vermilion border, and small jaw. Several other abnormalities, especially growth deficiency, were frequent but not constant. Chromosome analysis showed deletion of band 17p13 in 14 of 25 MDS probands. RFLP and somatic cell hybrid studies using probes from the 17p13.3 region including pYNZ22 (D17S5), pYNH37 (D17S28), and p144-D6 (D17S34) detected deletions in 19 of 25 probands tested including seven in whom chromosome analysis was normal. When the cytogenetic and molecular data are combined, deletions were detected in 21 of 25 probands. Parental origin of de novo deletions was determined in 11 patients. Paternal origin occurred in seven and maternal origin in four. Our demonstration of cytogenetic or molecular deletions in 21 of 25 MDS probands proves that deletion of a "critical region" comprising two or more genetic loci within band 17p13.3 is the cause of the MDS phenotype. We suspect that the remaining patients have smaller deletions involving the proposed critical region which are not detected with currently available probes.     

A Common Region of Deletion on Chromosome 17q in Both Sporadic and Familial Epithelial Ovarian Tumors Distal to BRCA1

Linkage analysis in familial breast and ovarian cancer and studies of allelic deletion in sporadic ovarian tumors have identified a region on chromosome 17q containing a candidate tumor-suppressor gene (referred to as BRCA1) of likely importance in ovarian carcinogenesis. We have examined normal and tumor DNA samples from 32 patients with sporadic and 8 patients with familial forms of the disease, for loss of heterozygosity (LOH) at 21 loci on chromosome 17 (7 on 17p and 14 on 17q). LOH on 17p was 55% (22/40) for informative 17pl3.1 and 17pl3.3 markers. When six polymorphic markers flanking the familial breast/ovarian cancer susceptibility locus on 17ql2-q21 were used, LOH was 58% (23/40), with one tumor showing telomeric retention. Evaluation of a set of markers positioned telomeric to BRCA1 resulted in the highest degree of LOH, 73% (29/40), indicating that a candidate locus involved in ovarian cancer may reside distal to BRCA1. Five of the tumors demonstrating allelic loss for 17q markers were from individuals with a strong family history of breast and ovarian cancer. More important, two of these tumors (unique patient number [UPN] 57 and UPN 79) retained heterozygosity for all informative markers spanning the BRCA1 locus but showed LOH at loci distal to but not including the anonymous markers CMM86 (D17S74) and 42D6 (D17S588), respectively. Deletion mapping of seven cases (two familial and five sporadic) showing limited LOH on 17q revealed a common region of deletion, distal to GH and proximal to D17S4, that spans −25 cM. These results suggest that a potential tumor-suppressor gene involved in both sporadic and familial ovarian cancer may reside on the distal portion of chromosome 17q and is distinct from the BRCA1 gene.     

Dosage effects on morphological and quantitative traits in maize aneuploids.

Dosage effects generated by either loss or gain of a chromosome segment were used to identify chromosome regions associated with morphological and quantitative characters in maize (Zea mays L.). Using B-A translocation stocks introgressed into a B73Ht background, a chromosome arm dosage series in a Mo17Ht x B73Ht F1 hybrid background was created for 18 of the 20 chromosome arms. The dosage series was then evaluated for 12 quantitatively inherited characters to associate specific phenotypic changes in a trait with a specific chromosome arm. Not only did our results show the familiar aneuploid syndrome phenomenon, but differential dosage effects among particular chromosome arms were demonstrated. All the quantitative traits measured and all the chromosome arms examined in this study were responsive to changes in chromosome arm dosage. The possible bases behind those differences and their utility in identifying quantitative trait loci, as well as the genetic relationships among the group of quantitatively inherited characters studied, are considered. Key words : corn, chromosome arm, B-A translocations, dosage analysis.     

Parental origin of the extra chromosome in Down's syndrome

Summary Chromosome 21 fluorescent heteromorphisms were studied in 42 patients with Down's syndrome, their parents and their siblings. Included in this number are two instances of an aunt and niece affected with trisomy 21, and one of affected siblings. One case has a de novo 21/21 translocation. Blood group, red cell and serum protein markers were also studied for linkage, gene exclusions, associations, and paternity testing. Thirty-one of the trisomy 21 cases were informative for parental origin of the extra chromosome and for stage of meiosis. The non-disjunctional event was of maternal origin in 24; 23 occurred in meiosis I, 1 in meiosis II. Seven were of paternal origin; 5 in meiosis I, and 2 in meiosis II. The translocation case was of paternal origin. A literature search revealed a total of 98 cases informative for the parent of origin of the extra chromosome, of >347 families tested. In addition, 3 de novo translocation cases, of 7 tested, were informative. The data suggest that most cases result from an error in the first meiotic division in the mother, but that a significant proportion are paternal in origin.