Regional localization on the human X of DNA segments cloned from flow sorted chromosomes

Nucleotide sequence and chromosomal mapping of the human c-yes-2 gene

We molecularly characterized the second gene, c-yes-2, of two copies of yes-related genes which we previously found to contain in the human genome. First, nucleotide sequence analysis revealed that the c-yes-2 gene is a pseudogene of the c-yes-1 gene. Second, by using two independent methods, hybridization of both DNAs from sorted chromosomes and metaphase spreads with c-yes-2 DNA, we assigned the c-yes-2 gene to chromosome 22q11.2. This chromosomal localization is consistent with that given in our previous report. The failure of proper mapping in our experiment might have been caused by instability of hybrid cell clones.

A restriction-fragment-length difference detected by the anonymous probe DXS199 exhibits non-Mendelian inheritance

Anonymous DNA probes were isolated from an X chromosome-enriched flow-sorted library. One of these probes, DXS199, identified a restriction-fragment difference that failed to show Mendelian segregation. All normal females were found to have two AvaII fragments of 6.5 kb and 6.0 kb, whereas all normal males had only the 6.5-kb fragment. DNA from a 49,XXXXY male was found to have both 6.0- and 6.5-kb AvaII fragments, in the same 3:1 ratio as seen in the inactive:active number of X chromosomes. This variant, which reflects a structural difference between active and inactive X chromosomes, is likely to be due to a methylation site on the active X chromosome.

Anonymous DNA probes to human chromosome 16 derived from a flow-purified library

Anonymous DNA probes specific for human chromosome 16 were isolated from a flow-purified human chromosome 16 library. The library was constructed at the Lawrence Livermore National Laboratory. Twenty-nine clones containing a unique or low-copy DNA insert were isolated. Of these, six were assigned to chromosome 16 and regionally mapped and 12 were shown not to map to chromosome 16. One clone mapped to 16pter----16p13.1, one clone to 16p11.1----16q13, one clone to 16q13----16q22.1, and three clones to 16q22.1----16q24. An additional clone from the same library was mapped to 16q13----16q22.1.

Evidence for linkage of Charcot-Marie-Tooth neuropathy (CMT1) to apolipoprotein A2 (Apo-A2)

We studied 169 members of 15 families with Charcot-Marie-Tooth neuropathy (CMT1) showing male-to-male transmission and slow motor-nerve conduction velocities. Four of these families were informative for linkage to apolipoprotein A2 on chromosome 1 (1q21-23) with an overall lod score of 2.45 at theta = .001. There was no statistical evidence of genetic heterogeneity.

Identification and sorting of micronuclei containing individual chromosomes

Micronuclei are diploid genome subfractions which can be induced by colchicine treatment. The purpose of the present study was to identify the chromosome content of micronuclei. Accordingly, PtK1 cells were micronucleated with colchicine and their DNA was labeled by the Hoechst 33342 fluorochrome. The fluorescence intensity of the micronuclei was measured by flow cytometry and compared to that of metaphase chromosomes of the same species. We observed histograms exhibiting five distinct peaks for both micronuclei and chromosomes. Each class of micronuclei corresponded to a peak in the flow karyotype with the same values. As the smallest micronuclei contained the same amount of DNA as one chromosome, it seemed possible to identify the DNA content of the micronuclei containing a single chromosome. This identification was confirmed by fluorescence microscope observations of the micronuclei and chromosomes sorted from their respective peaks. This was clear for peak number 3, which exhibited fluorescent markers both in micronuclei and in chromosomes. These markers, called chromocenters, were connected with the nucleoli in micronuclei and were specific for the nucleolar organizer regions of the X chromosomes. As we paid particular attention to maintaining the transcriptional activity of the micronuclei throughout the procedure used to sort and identify them, it is concluded that such an approach might be very suitable for investigating the expression of reduced nuclear domains corresponding to individual chromosomes.

Linked polymorphic DNA markers in the prediction of X-linked muscular dystrophy

Ten polymorphic DNA markers, including gene specific markers of loci DXS164 and DXS206, were tested for allele frequencies, degree of heterozygosity and linkage in 34 Finnish families with X-linked muscular dystrophy. With the exception of the BamHI RFLP of DXS164 subclone pERT87-15, allele frequencies and the degree of heterozygosity failed to show any significant deviation from the data published elsewhere. We document a high degree of linkage disequilibrium between several RFLPs belonging to locus DXS164. Our linkage data include one recombination between DMD and DXS164 enabling a tentative location of the mutation site distal to DXS164. The maximum lod score for linkage between the disease locus and DX164 was 7.828 at a recombination fraction of 0.02. According to our data DXS28 and DXS43 may be located further away from the disease locus than previously thought. We use only gene specific markers for genetic counselling. Excluding deletions, 97.1% of women were heterozygous for at least one such marker. A diagnostic procedure in which useful information can be obtained in over 90% of all diagnostic situations, using only four filters, is proposed.

Linkage relationships between X-linked retinitis pigmentosa and nine short-arm markers: exclusion of the disease locus from Xp21 and localization to between DXS7 and DXS14

Linkage data between X-linked retinitis pigmentosa (XLRP) and nine X-chromosomal markers are reported. To test the assignment of XLRP to the Xp21 region (as considered at Human Gene Mapping 8), an analysis of XLRP and six markers flanking this region was undertaken. The XLRP locus was found to be excluded from the chromosome distal to ornithine transcarbamylase (OTC) (P = 6.5 X 10(-5]. Further data were accumulated with three more probes proximal to DXS7 (L1.28), the closest linked probe. Multipoint analysis of these data suggests a posterior probability of .94 that XLRP is proximal to DXS7 (L1.28), which has been mapped to the region Xp11.3.

Construction of a chromosome 16-enriched phage library and characterization of several DNA segments from 16p

A flow sorted chromosome 16-enriched recombinant library was produced to isolate DNA probes useful for constructing a linkage map of 16p, primarily for the study of adult polycystic kidney disease (APKD). The APKD locus has been mapped to chromosome 16 by linkage with the probe 3'HVR, which is located in the region 16p12----pter. Of the 48 single-copy fragments isolated from this new phage library, 39 (81%) were found to be chromosome 16 specific. Probes mapping to chromosome 16 were regionally localized by hybridizing to flow-sorted spot blots of translocation products from lymphoblastoid cell lines containing the rearrangements t(1;16) or t(11;16). Translocation breakpoints at 16p13.11 and 16p11.1 were utilized to subdivide chromosome 16 into three regions: Twenty-six probes were mapped to 16p11.1----16qter, two to 16p11.1----16p13.11, and eleven to 16p13.11----16pter. Probes from 16p were examined for their recognition of restriction fragment length polymorphisms (RFLPs). Seven polymorphic probes were found which recognized eleven RFLPs. Six of the seven probes have RFLPs which are reasonably informative (polymorphism information contents (PIC) of over 0.25). Two of these identify polymorphisms with three different alleles, one of which has a PIC value of over 0.4. These probes may aid in the diagnosis of APKD and contribute towards a linkage map of chromosome 16.

Linkage analysis of Charcot-Marie-Tooth neuropathy (HMSN type I)

Fifteen HMSN families with 218 members and documented male-to-male transmission and slow motor nerve conduction velocities were informative for linkage to Duffy blood group (Fy), antithrombin III cDNA probe (AT3) and renin (REN). Our data support linkage to Fy in 8 families (lod score = 2.45 at theta = 0) consistent with HMSN type IB. Linkage to AT3 (lod score = 1.28 at theta = 0) and linkage of Fy to AT3 (lod score = 1.61 at theta = 0) is also supported in 3 of the 8 original families. Linkage to REN (lod score = 0.78 at theta = 0), linkage of Fy to REN (lod score = 0.89 at theta = 0), and linkage of AT3 to REN (lod score = 0.88 at theta = 0) is supported in only 2 of the 8 original families. Linkage to Fy was rejected in seven families, consistent with HMSN type IA (lod score = -4.34 at theta = 0.05). Linkage to AT3 was rejected in 12 families (lod score = -9.52 at theta = 0.05). Linkage to REN was rejected in 13 families (lod score = -11.07 at theta = 0.05). Our data provide support for the concept of genetic heterogeneity in CMT hypertrophic neuropathy (HMSN type I). The linkage of HMSN type IB to Fy seems to be tighter than to AT3 and REN, strongly suggesting the mapping of HMSN type IB locus on the proximal part of the long arm of chromosome 1, close to the centromere.

DNA studies in a family with Duchenne muscular dystrophy and a deletion at Xp21

We have performed Southern blot analysis on a large, four-generation kindred with Duchenne muscular dystrophy (DMD). Probes 754 (DXS 84), pERT87-1, pERT87-8, pERT87-15 (DXS164), and pXJ-1.1 did not hybridize to digested genomic DNA of affected males. Obligate-carrier mothers and unaffected brothers showed signals of a single X-chromosome copy intensity, and suspected noncarrier sisters demonstrated either a single band of two-copy intensity or informative polymorphisms. Uniform hybridization was seen with probes C7 (DXS28) and D2 (DXS43), which map distal to the DMD locus, and with OTC, which maps proximally. This deletion was present in six affected individuals and has been transmitted through 3 generations to date. On high-resolution chromosome analysis, a deletion within band Xp21 was consistently observed in one affected male studied and in one of the two X chromosomes in obligate carriers. This large molecular and cytogenetically visible deletion in affected DMD individuals without glycerol kinase deficiency, chronic granulomatous disease, retinitis pigmentosa (RP), or ornithine transcarbamylase deficiency is a very rare finding and should prove useful in specifically cloning additional probes within and flanking the DMD locus.

Complete cloning of the Duchenne muscular dystrophy (DMD) cDNA and preliminary genomic organization of the DMD gene in normal and affected individuals

The 14 kb human Duchenne muscular dystrophy (DMD) cDNA corresponding to a complete representation of the fetal skeletal muscle transcript has been cloned. The DMD transcript is formed by at least 60 exons which have been mapped relative to various reference points within Xp21. The first half of the DMD transcript is formed by a minimum of 33 exons spanning nearly 1000 kb, and the remaining portion has at least 27 exons that may spread over a similar distance. The DNA isolated from 104 DMD boys was tested with the cDNA for detection of deletions and 53 patients exhibit deletion mutations. The majority of deletions are concentrated in a single genomic segment corresponding to only 2 kb of the transcript.

Disease diagnosis by recombinant DNA methods

Recombinant DNA procedures have now been applied to the problem of the identification of molecular defects in man that account for heritable diseases, somatic mutations associated with neoplasia, and acquired infectious disease. Thus recombinant DNA technology has rapidly expanded our ability to diagnose disease. Substantial advances in the simplification of procedures for diagnostic purposes have been made, and the informed physician has gained in diagnostic accuracy as a consequence of these developments. The wide application of recombinant DNA diagnostics will depend on simplicity, speed of results, and cost containment.

Linkage of the Wiskott-Aldrich syndrome with polymorphic DNA sequences from the human X chromosome

The Wiskott-Aldrich syndrome (WAS) is one of several human immunodeficiency diseases inherited as an X-linked trait. The location of WAS on the X chromosome is unknown. We have studied 10 kindreds segregating for WAS for linkage with cloned, polymorphic DNA markers and have demonstrated significant linkage between WAS and two loci, DXS14 and DXS7, that map to the proximal short arm of the X chromosome. Maximal logarithm of odds (lod scores) for WAS-DXS14 and WAS-DXS7 were 4.29 (at theta = 0.03) and 4.12 (at theta = 0.00), respectively. Linkage data between WAS and six marker loci indicate the order of the loci to be (DXYS1-DXS1)-WAS-DXS14-DXS7-(DXS84-OTC). These results suggest that the WAS locus lies within the pericentric region of the X chromosome and provide an initial step toward identifying the WAS gene and improving the genetic counseling of WAS families.

Efficient isolation of X chromosome-specific single-copy probes from a cosmid library of a human X/hamster hybrid-cell line: mapping of new probes close to the locus for X-linked mental retardation

We isolated X-chromosomal DNA probes from a cosmid library constructed from a single human X/hamster hybrid-cell line (C12D). One hundred human clones were isolated and used to construct a pool of X-chromosomal DNA. This DNA was digested into 0.15-2-kb fragments and subcloned into plasmids allowing the rapid characterization of new single-copy probes. These were regionally mapped and used for the detection of restriction-site polymorphisms. Together with a series of subcloned probes from individually isolated cosmids, we found seven polymorphic probes among 53 tested. Thirty-one of the probes were physically localized to different regions of the X chromosome. Four polymorphic probes map to Xq27-Xq28: DXS102 (cX38.1), DXS105(cX55.7), DXS107(cpX234), and DXS134(cpX67). These were genetically mapped by multipoint analysis relative to previously characterized loci, a mapping that resulted in the following order: DXYS1, DXS107, DXS51/DXS102, F9, DXS105, Fra-X, F8/DXS52, DXS15, DXS134. The mapping of DXS105 between F9 and Fra-X makes this probe useful for Fra-X analysis. For the linkage between FraX and DXS105, a maximum lod score of 5.01 at 4 cMorgans has been obtained in one large Dutch pedigree.

Two RFLPs identified by an anonymous sequence (D7S19) (pTS119) from chromosome 7

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Molecular analysis of human muscular dystrophies

The ability to map disease loci using restriction fragment length polymorphisms (RFLPs) identified by DNA probes has revolutionized molecular genetics. Duchenne and Becker muscular dystrophies have been shown to be localized within the same very small region of Xp21 on the human X chromosome. The mutation itself should soon be identified at the DNA level, which will permit a detailed analysis of the molecular defect at the biochemical level. Rapid progress has also been made in the study of myotonic dystrophy on chromosome 19. DNA markers closely linked to the mutant locus have been identified, making antenatal diagnosis possible in informative families. Autosomal recessive muscular dystrophies are more difficult to study, but the means to localize even these mutations is being developed. The next decade should prove to be an exciting one for those involved in the molecular analysis and clinical management of human muscular dystrophies.

Rapid cloning of multiple amplified nucleotide sequences from human neuroblastoma cell lines by phenol emulsion competitive DNA reassociation

A protocol for the rapid cloning of many DNA fragments from an amplified genomic region is described. The procedure is based on a modification of the phenol-emulsion reassociation technique (PERT) previously used to clone DNA fragments missing from a chromosomal deletion [Kunkel et al., Proc. Natl. Acad. Sci. USA 82 (1985) 4778-4782]. The procedure was used to construct recombinant libraries in the plasmid pBR322 which were highly enriched for amplified sequences from two neuroblastoma cell lines, CHP-126 and IMR-32. Many new amplified DNA fragments were isolated from these libraries, indicating that the PERT methodology should be of general use in isolating amplified DNA from other cell lines and tumors.

Localization of a novel v-erbB-related gene, c-erbB-2, on human chromosome 17 and its amplification in a gastric cancer cell line

The c-erbB-2 gene is a v-erbB-related proto-oncogene which is distinct from the gene encoding the epidermal growth factor receptor. By using two independent methods, hybridization of both sorted chromosomes and metaphase spreads with cloned c-erbB-2 DNA, we mapped the c-erbB-2 locus on human chromosome 17 at q21, a specific breakpoint observed in a translocation associated with acute promyelocytic leukemia. Furthermore, we observed amplification and elevated expression of the c-erbB-2 gene in the MKN-7 gastric cancer cell line. These data suggest possible involvement of the c-erbB-2 gene in human cancer.

A genetic linkage study of choroideremia

One hundred and twenty-two members of 15 choroideremia families have been used in a genetic linkage study of choroideremia (TCD) using four DNA probes situated on the X chromosome. Linkage was analysed using DNA probes DXS14 (p58-1), DXYS1 (pDP 34), DXS178 (p212) and DXS177 (lambda 2.7). Statistically significant linkage was demonstrated with DXYS1 (theta = 0.00, lod 4.95), in agreement with the findings of Nussbaum et al. (1985). Evidence consistent with loose linkage to TCD was also found with DXS14 (theta = 0.31, lod 0.23), DXS178 (theta = 0.18, lod 1.41) and DXS177 (theta = 0.27, lod 0.20). The results suggest that TCD is located in the region Xq13-q21. Probe DXYS1 is likely to prove useful in the prenatal diagnosis of this condition.

DNA analysis in human disease

The analysis of human DNA using recombinant DNA technology is fast becoming an integral part of the diagnosis, assessment, and prevention of inherited and somatic genetic disease. The rationale underlying these methods of analysis is discussed, and the nature and extent of mutational change in heritable disorders and neoplastic development is outlined.

Linkage studies in Duchenne and Becker muscular dystrophies

We have studied the inheritance of four cloned DNA sequences which recognise restriction fragment length polymorphisms on the short arm of the X chromosome in families with Becker and Duchenne muscular dystrophy. We have confirmed linkage of two probe loci to the disease loci and have combined our results with those previously published to give a maximum lod score of 11.642 at a recombination fraction of 0.15 for DXS41 (probe 99.6), and a maximum lod of 15.84 at a recombination fraction of 0.15 for DXS84 (probe 754). Linkage of these diseases to the loci defined by the pERT87 probes and probe pXJ1.1 has also been studied, giving maximum lod scores of 8.634 and 5.118 at recombination fractions of 0.02 and 0.00 respectively. The information obtained using these polymorphic DNA markers, combined with pedigree and CK data, can be used to give more accurate genetic counselling to women at risk in Becker and Duchenne families.

Carrier detection and prenatal diagnosis in X linked muscular dystrophy using restriction fragment length polymorphisms

With the aim of offering carrier detection, genetic counselling, and prenatal diagnosis to as many families with Duchenne (DMD) and Becker (BMD) muscular dystrophy as possible, we used available DNA probes to determine the usefulness of the RFLP approach. We report in detail the risks calculated using Bayesian theory and combining pedigree and creatine kinase (CK) data with information derived from the RFLP studies. To date we have analysed members of 28 DMD families (10 familial, 18 sporadic) and six BMD families (four familial, two sporadic) with the closely linked pERT probes 87-1, 87-8, and 87-15 (DXS164). In addition, key members of all families were analysed with probes D2 (DXS43), C7 (DXS28), 754 (DXS84), and L1 X 28 (DXS7). Of the 97 females at risk of being carriers (not including 26 obligate carriers), the RFLP results were compatible with carriership in 22 and not in 51. In 24 females (including 17 mothers of sporadic cases), no information regarding carriership was derived from the RFLP studies. There was no disagreement between pedigree information, clearly raised CK values, and DNA studies. Of 52 obligate or possible carriers under the age of 45, prenatal diagnosis is possible in 49. Prenatal diagnostic RFLP studies have so far been done in three women. In one sporadic DMD family and one BMD family with three affected males the probands showed a deletion involving the three pERT87 subclones used. Experience derived from these families indicates that in our society genetic counselling in X linked muscular dystrophy is received with approval or even enthusiasm in spite of the 5% error estimate that we have quoted for pERT87 derived results.

Mapping by chromosome sorting of several gene probes, including c-myc, to the derivative chromosomes of a 3;8 translocation associated with familial renal cancer

In eight members of a single family a constitutional translocation t(3;8) (p14.2;q24.1) is associated with the development of renal cancer. Chromosomes isolated from a cell line established from a subject with this translocation were analysed in flow with a fluorescence-activated cell sorter (FACS II). Nearly six million chromosomes from the flow karyotype region containing the der(8) and 5.5 million from the region containing the der(3) were sorted, the DNA extracted, digested with EcoRI, size fractionated by electrophoresis, and transferred to nitrocellulose. Hybridization with gene probes for c-mos, which has been localized to 8q11-q22 and somatostatin, which has been mapped to 3q28, confirmed that the sorted fractions contained, respectively, the der(8) and der(3) chromosomes. The cellular oncogenes c-raf-1 (3p25) and c-myc (8q24) were found to be translocated to the der(8) and der(3) chromosomes, respectively. The possible role that the relocation of c-myc might have on the development of renal carcinoma in carriers of this 3;8 translocation was further studied by analysis of the region surrounding the c-myc gene. By the use of cosmid cloning, no rearrangement 31 Kb 5'(or 19 Kb 3') of the translocated gene was found, indicating that the break-point is not immediately adjacent to c-myc. In an associated study, the DNA fragment D3S2 from chromosome 3 was found to map to 3p14.2-pter. This assignment in conjunction with published somatic cell hybrid data enabled D3S2 to be mapped more precisely to the interval 3p14.2-3p21.

Close linkage between X-linked ectodermal dysplasia and a cloned DNA sequence detecting a two allele restriction fragment length polymorphism in the region Xp11-q12

EDA (ectodermal dysplasia, anhidrotic) is an X-linked recessive disorder characterized by hypohidrosis, hypoor anodontia, and hypotrichosis. A possible linkage between the gene for EDA and a number of restriction fragment length polymorphisms (RFLPs) spread over the X chromosome was investigated in two Danish families segregating EDA. No recombination between the gene for EDA and our probe pTAK8, which detects a two allele polymorphism in the region Xp11-q12, was found in nine informative meiotic events (seven of which are phase known), giving a maximal lod score of 2.41 at a recombination fraction of 0.00. This juxtacentromeric location of the gene for EDA agrees well with the linkage data obtained with the other markers used in this study.

The X chromosome shows less genetic variation at restriction sites than the autosomes

Using a standard technique, 122 single-copy probes were screened for their ability to detect restriction fragment length polymorphisms (RFLPs) in the human genome. The use of a standardized RFLP screening enables the introduction of statistical methods in the analysis of differences in RFLP content between chromosomes and enzymes. RFLPs were detected from panels containing at least 17 unrelated chromosomes, digested with TaqI, MspI, BglII, HindIII, EcoRI, and PstI. Forty autosomal probes, representing a sample of 2,710 base pairs (bp) per haploid genome, were tested, and 24 RFLPs were found. With 82 X-chromosomal probes, 17 RFLPs were found in 6,228 bp per haploid genome. The frequency of X-chromosomal RFLPs is three times less than that of the autosomes; this difference is highly significant (P = less than .001). The frequency of RFLPs revealed by various restriction enzymes and the possibility that the X chromosome is a "low mutation" niche in the human genome are discussed.

Repeated DNA sequences in the distal long arm of the human X chromosome

Two DNA probes from within a single large insert from a recombinant phage-DNA library that was constructed from flow-sorted chromosomes enriched for the human X chromosome were shown to hybridize with repeated X-specific and autosomal DNA sequences. The X-chromosomal repeated sequences were assigned to the distal long arm of the X chromosome by both hybrid mapping and in situ hybridization. Fine mapping places these repeats in a region of Xq28 between DX13 (DXS15, in distal Xq28) and factor VIII (F8C, in proximal Xq28). The location of the X-specific repeats makes them potentially useful for future investigations of diseases mapping to the distal long arm of the X chromosome, such as the fragile X syndrome.

Construction, analysis, and application to 46,XY gonadal dysgenesis of a recombinant phage DNA library from flow-sorted human Y chromosomes

The analysis of a recombinant human Y-enriched Hind III total digest phage library prepared from the DNA of flow sorted human Y chromosomes is described. Out of 43 phage inserts from the library thus far mapped, 25 revealed hybridization with Y chromosomal DNA. These inserts may be divided into five groups according to their degree of Y specific hybridization: inserts that hybridize with one single copy or slightly repeated Y-specific DNA sequence, Y-specific repeated sequences of various restriction fragment lengths, Y-chromosomal DNA sequence(s) shared by a sequence on the X and/or on autosomes, Y-specific DNA sequences in addition to multiple X and/or autosomal sequences, or Y-specific repeated DNA in addition to multiple X and/or autosomal sequences. Application of probes from this library for diagnostic purposes is shown in two 46,XY patients with gonadal dysgenesis and small deletions of the Y short arm.

Construction and analysis of an EMBL-3 phage library containing partially digested human chromosome 21-specific DNA inserts (15-20 kb)

In the mouse-human hybrid cell line SCC 16-5, chromosome 21 is the only human chromosome present. Fractions highly enriched for this chromosome were obtained by applying the chromosome velocity sedimentation technique to this cell line. DNA prepared from these chromosomal fractions was partially digested with Mbo I, size fractionated on an NaCl gradient, and cloned in the EMBL-3 phage vector. The phage library thus prepared was highly enriched for human chromosome 21-specific recombinant DNA sequences 15-20 kb long. Of the approximately 21,000 phage clones obtained, at least 99% were recombinant. Following phage plaque filter hybridization and Southern blotting, it was found that half of the recombinants were positive for human repetitive DNA. Almost all phages harbored highly or middle repetitive human or mouse DNA sequences owing to the large size of the recombinant inserts. In this library, the human chromosome 21 is represented approximately four times. All human recombinants studied thus far contained DNA inserts originating from chromosome 21 only. The employed cloning strategy is discussed with regard to utility, purity, quality, and completeness of chromosome-specific recombinant DNA libraries.

Deletion mapping of the testis determining locus with DNA probes in 46,XX males and in 46,XY and 46,X,dic(Y) females

Eleven Y-specific DNA probes hybridizing with DNA from one or more 46,XX males were isolated from a recombinant phage DNA library constructed from flow sorted human Y chromosomes. Two probes hybridized with DNA from nine out of eleven, i.e. greater than 80% of these 46,XX males. The relative frequency of hybridization of the probes in the 46,XX males and in a 46,X,dic(Y) female, together with in situ hybridization data, allowed mapping of the probes on Yp in relation to a putative testis determining locus. Several of those probes were also absent in a 46,XY female, further refining a model for ordering the probes on Yp. The DNA of one XX male hybridized both with probes from Yp and probes from proximal Yq (excluding the pericentral region). This suggests that complex translocations may occur into the DNA of 46,XX males that involve not only parts of Yp but also parts of Yq.

Regional assignment of Y-linked DNA probes by deletion mapping and their homology with X-chromosome and autosomal sequences

A series of Y recombinants have been isolated from Y-specific DNA libraries and regionally located on the Y chromosome using a Y deletion panel constructed from individuals carrying structural abnormalities of the Y chromosome. Of twenty recombinants examined twelve have been assigned to Yp and eight to Yq. Five of the Yp recombinants map between Yp11.2 and Ypter and one can only be assigned to Yp. Of the former, four detect homologies on the X chromosome between Xq13 and Xq24 and the latter one between Xp22.3 and Xpter. The sixth recombinant detects autosomal homologous sequences. The six remaining Yp probes are located between Ycen and Yp11.2. One of these detects a homology on the X chromosome at Xq13-Xq24 and a series of autosomal sequences, two detect uniquely Y-specific sequences and three a complex pattern of autosomal homologies. The remaining eight recombinants have been assigned to three intervals on Yq. Of three recombinants located between Ycen and Yq11.21 two detect only Y sequences and one additional autosomal homologies. Two recombinants lie in the interval Yq11.21-Yq11-22, one of which detects only Y sequences and the other an Xp homology between Xp22.3 and Xpter. Finally, the three remaining Yq recombinants all detect autosomal homologies and are located between Yq11.22 and Yq12. The divergence between homologies on different chromosomes has been examined for three recombinants by washing Southern Blots at different levels of stringency. Additionally, Southern analysis of DNA from flow sorted chromosomes has been used to identify autosomes carrying homologies to two of the Y recombinants.

Identification and application of additional restriction fragment length polymorphisms at the human ornithine transcarbamylase locus

Two additional restriction fragment length polymorphisms (RFLPs) have been identified at the human ornithine transcarbamylase (OTC) locus. Approximately 11% of women are heterozygous for an RFLP characterized by polymorphic bands at 3.7 and 3.6 kilobasepairs (kbp) observed after DNA digestion with TaqI. Twenty-nine percent of women are heterozygous for an RFLP characterized by polymorphic bands at 18.0 and 5.2 kbp observed after digestion with BamHI. Thus, in combination with the previously reported RFLPs identified using MspI, the X chromosomes in approximately 80% of women at risk for having a son with OTC deficiency are distinguishable by RFLPs at the OTC locus. Furthermore, we show that these RFLPs will be useful in families for prenatal diagnosis of OTC deficiency, carrier detection, and carrier exclusion.

Clinical applications of gene probes in human genetic disease, malignancy, and infectious disease

Recent developments in recombinant DNA technology have made possible the production of gene probes consisting of cloned gene segments, cloned segments of DNA linked to genes, and synthetic gene fragments. Several methods have been developed by which these probes may be used for the diagnosis of human disease. This technology has been outstandingly successful for prenatal diagnosis and carrier detection in many genetic diseases. These methods have also been successfully applied to the analysis of human malignancies, by providing for the determination of cell lineage and clonality in lymphoid neoplasms. Finally, these methods have shown potential for rapid and sensitive diagnosis of some infectious diseases.

DNA linkage analysis of X chromosome-linked chronic granulomatous disease

Chronic granulomatous disease (CGD) is a disorder of phagocytes that is usually inherited as an X chromosome-linked trait. Previous family studies suggested that the CGD locus resides on the distal short arm (Xp22-Xpter). Using cloned, polymorphic DNA probes we have performed a linkage analysis within CGD families that suggests a more proximal location (Xp21). In addition, the CGD locus is proximal to the Duchenne muscular dystrophy locus and lies within a broad region of Xp in which recombination appears to be greater than anticipated on the basis of physical distance between markers. Regional localization of the X chromosome CGD locus should facilitate molecular cloning of the CGD gene and molecular dissection of the phagocyte oxidase system.

Quantitative analysis of sex-chromosome mosaicism with X-Y DNA probes

Sex-chromosome mosaicism was quantitatively analyzed in two patients using DNA probes specific for human X and Y chromosomes. Both patients were female with stigmata of the Turner syndrome, and both had a 45,X cell line and a 46,XY cell line. One of the patients had a morphologically abnormal, nonfluorescent Y chromosome, dic(Y)(q11). Hybridization of DNA from this patient with two repetitive DNA sequences specific for the heterochromatic region of the Y chromosome indicated that most of the Y-heterochromatic sequences were deleted. DNA from both patients was hybridized with a probe for the DXYS1 locus and found to have the X- and Y-linked loci. Densitometric measurements of the relative intensities of the X- and Y-linked bands were used to calculate the degree of mosaicism in each case. The percentages of 45,X cells obtained by DNA analysis agreed with those obtained by chromosome analysis. DNA analysis provides a way to quantitate mosaicism at the DNA level and in nondividing tissue.

Cloning of DNA libraries from mouse Y chromosomes purified by flow cytometry

To purify mouse Y chromosomes by flow cytometry, a male cell line containing the Robertsonian translocation Rb(9.19)163H has been established by SV40 transformation. Flow karyotypes obtained from these cells exhibit a well-isolated peak of fluorescence corresponding to the single Y chromosome, clearly distinct from that of chromosome 19. From this peak, 650,000 chromosomes were sorted, and two restriction fragment libraries were constructed from the DNA of the sorted chromosomes. The characterization of several Y-specific fragments has shown that the Y DNA was enriched at least 36-fold. Furthermore, given that there are likely homologies between the X and Y chromosomes, we can assume that this calculated value of the purification factor is an underestimation and that the Y DNA was more highly purified by flow sorting.

Localization of a novel v-erbB-related gene, c-erbB-2, on human chromosome 17 and its amplification in a gastric cancer cell line

The c-erbB-2 gene is a v-erbB-related proto-oncogene which is distinct from the gene encoding the epidermal growth factor receptor. By using two independent methods, hybridization of both sorted chromosomes and metaphase spreads with cloned c-erbB-2 DNA, we mapped the c-erbB-2 locus on human chromosome 17 at q21, a specific breakpoint observed in a translocation associated with acute promyelocytic leukemia. Furthermore, we observed amplification and elevated expression of the c-erbB-2 gene in the MKN-7 gastric cancer cell line. These data suggest possible involvement of the c-erbB-2 gene in human cancer.

Moderately repeated DNA sequences specific for the short arm of the human Y chromosome are present in XX males and reduced in copy number in an XY female

Four DNA sequences specific for the Y chromosome were isolated from a recombinant phage library constructed from flow sorted human Y chromosomes. Two of these sequences were moderately repeated and assigned to the short arm of the Y chromosome by in situ hybridization. Both sequences were detected in five out of six [corrected] 46,XX males and were reduced in copy number in one out of two 46,XY gonadal dysgenesis patients tested. The findings suggest close proximity of these Y-specific moderately repeated DNA sequences to a testis determining locus.

Mapping of the X-linked agammaglobulinemia locus by use of restriction fragment-length polymorphism

A molecular linkage analysis in 11 families with X-linked agammaglobulinemia (XLA) localized the XLA gene to the proximal part of the long arm of the human X chromosome. Significant linkage was detected between XLA and loci defined by two polymorphic DNA probes called 19-2 for the DXS3 locus and S21 for the DXS17 locus. Both localize to the region Xq21.3-Xq22. Most likely recombination distances (theta) and associated logarithm of the odds (lod) scores for the XLA-DXS3 and XLA-DXS17 pairs were theta = 0.04 morgans (lod, 3.65) and theta = 0 (lod, 2.17), respectively. Tight linkage between XLA and the locus DXS43 defined by the X short arm probe D2 (localized to Xp22-Xp21) was strongly excluded and we obtained no evidence for significant linkage between XLA and any other X short arm probe. The probe pair 19-2 and S21 should be informative for molecular linkage-based analysis of XLA segregation in the majority of families afflicted with this disorder.

Chromosomal assignment of human genes for gastrin, thyrotropin (TSH)-beta subunit and C-erbB-2 by chromosome sorting combined with velocity sedimentation and Southern hybridization

Human genes for gastrin, thyrotropin (THS)-beta subunit and c-erbB-2 were assigned to specific chromosomes using a single-laser cell sorter. For this purpose, condensed human chromosomes prepared from a karyotypically normal lymphoblastoid cell line were preliminarily fractionated by velocity sedimentation, and then sorted using a fluorescence-activated cell sorter. DNA was then extracted from the chromosomes, cleaved by restriction enzymes, and subjected to Southern hybridization using gene-specific radioactive probes. When the assignment of specific chromosomes was not possible due to chromosomal size overlapping, sorted chromosomes from cell lines carrying chromosomal translocation or from hybrid cells carrying known human chromosomes were used in addition. The results indicate that human genes for gastrin, TSH-beta, and c-erbB-2 are located on chromosomes 17, 1 and 17, respectively.

Cytological, flow cytometric, and molecular analysis of the rapid evolution of mammalian chromosomes containing highly amplified DNA sequences

Transfection of a mouse dihydrofolate reductase (DHFR) cDNA contained in a plasmid "expression vector" into DHFR deficient Chinese hamster cells, followed by progressive selection of cells in increasing concentrations of methotrexate (MTX), leads to marked amplification of the exogenous DHFR sequences in the recipient hamster cells. This gene amplification is evident at the cytological level, in the form of homogeneously staining chromosomal regions (HSRs), at a gene expression level, in the form of fluorescein-methotrexate binding, and at the DNA level. Flow sorting, based on variable fluorescein-MTX binding, or direct cellular cloning, followed by chromosome analysis, revealed intercellular heterogeneity of HSRs in size and distribution. This suggested that there was a rapid evolution of HSRs in MTX-resistant transfectants. Chromosomal analysis of HSR evolution in situ, by examining individual colonies presumably derived from one or a few cells, underscored this impression of chromosome structural fluidity. Rates of HSR change in excess of 0.01 per cell division, increased by low doses of the recombinogen, mitomycin C, were detected. The Chinese hamster DHFR transfectants described should be amenable to detailed, coordinate cytological and molecular characterization. Such an analysis should contribute to an understanding of processes such as homologous recombination in mediating HSR evolution in mammalian chromosomes.

Human chromosome 21-encoded cDNA clones

We have employed two strategies to isolate random cDNA clones encoded by chromosome 21. In the first approach, a cDNA library representing expressed genes of WA17, a mouse-human somatic cell hybrid carrying chromosome 21 as its sole human chromosome, was screened with total human DNA to identify human chromosome 21-specific cDNAs. The second approach utilized previously characterized single-copy genomic fragments from chromosome 21 as probes to retrieve homologous coding sequences from a human fetal brain cDNA library. Six cDNA clones on chromosome 21 were obtained in this manner. Two were localized to the proximal long arm of chromosome 21, two to the distal portion of the long arm, and one to the region of 21q22 implicated in the pathology of Down syndrome.

Detection of DNA sequences in nuclei in suspension by in situ hybridization and dual beam flow cytometry

This report describes the fluorescence hybridization of DNA sequence probes to interphase nuclei in suspension and the quantification of bound probe by dual beam flow cytometry. Nuclear proteins were first cross-linked with dimethylsuberimidate to prevent disintegration of the nuclei during denaturation and hybridization. To demonstrate that in situ hybridization can be performed in suspension, stabilized mouse thymocyte nuclei were hybridized with a probe for mouse satellite DNA sequences. The DNA probes were labeled with 2-acetylaminofluorene. After hybridization, an indirect immunofluorescent labeling procedure was used to visualize the target sequences. With dual beam flow cytometry, both the amount of hybridized probe and the DNA content of individual nuclei were determined. Thus, the specificity of DNA hybridization can be combined with the speed and quantitative analysis provided by flow cytometry.