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We report a collection of tri- and tetranucleotide repeat sequence polymorphic markers used to construct genome-wide human linkage maps. Using a strategy of marker selection to create libraries highly enriched for the presence of specific tandem repeat elements, we have developed over 2000 high heterozygosity, easy-to-use tri- and tetranucleotide short tandem repeat polymorphisms (STRPs). To date, over 1300 of these markers have been genotyped on the CEPH reference families. Additional STRPs were assigned to chromosomes using human monochromosomal somatic cell hybrids. The linkage maps constructed with these markers have been integrated with other CEPH genotypes into a comprehensive high density linkage map. These STRPs have been shown to be robust for genotyping in a variety of laboratories using a variety of methods. The high quality of these STRPs makes them ideal candidates for use in genome-wide linkage searches. The integration of these markers with physical mapping reagents and other genetic markers will create a resource for moving from genome-wide linkage searches to rapid sublocalization of disease loci.

Linkage analysis can be used to test the hypothesis that a marker locus of known location segregates independently from a presumed disease gene. One way to test this hypothesis is to measure the similarity of marker alleles among pairs of relatives affected with the disease. When the disease under consideration is cancer, it is possible to take advantage of the marker alleles in tumors to revise the similarity measure obtained from the observations made in constitutional tissue. Only cancers that arise through the model of recessive oncogenesis are amenable to this revised analysis. This model postulates that cancer is caused by somatic genetic changes which result in the loss of one or both copies of a normal allele at a tumor suppressor locus. If an individual's inherited genotype is heterozygous at the marker locus, the model of recessive oncogenesis suggests that we may observe loss of constitutional heterozygosity at the marker locus in the tumor. In this report, we how how to incorporate this loss of heterozygosity data into affected pedigree member linkage tests. The revised procedure is illustrated using data obtained from relatives with breast cancer. Substantial improvement in the power to reject the different chromosome hypothesis is obtained when loss of heterozygosity is observed in multiple relatives with the same marker alleles retained in the tumors.

The ability to detect or reject genetic linkage in studies of human cancer is often diminished because multiple affected relatives in a pedigree are unavailable for analysis. The observation of somatic allele loss in tumors can provide knowledge about gametic phase. Therefore, consideration of tumor genotype data could be used to obtain knowledge about gametic phase ordinarily gained from a larger sample of individuals in cancer families. The objective of the present study is to describe a method for improving the power to detect or reject genetic linkage by using knowledge about somatic genetic changes in tumor tissue. A modification to the lod score method of linkage analysis is proposed in which knowledge of gametic phase in the linkage likelihood is inferred from observations of loss of constitutional heterozygosity (LoH) in tumor tissue. This methodology was evaluated using a double backcross nuclear family with a pair of offspring. The expected lod score improved substantially when tumor genotype data were included in the analysis. For example, when the haplotype remaining in tumor tissue was identical to the inherited haplotype in constitutional tissue 99% of the time, linkage analyses without tumor genotype data would require a 2-5 times larger sample of offspring pairs to conclude linkage with an expected lod score value of 3 or greater, compared to analyses incorporating tumor genotype data. These results suggest that consideration of tumor genotype data using the proposed method can substantially improve the power of linkage analyses in cancer families.

Fasioscapulohumeral muscular dystrophy (FSHD) has recently been localized to 4q35. We have studied four families with FSHD. Linkage to the 4q35 probes D4S163, D4S139, and D4S171 was confirmed. We found no recombinants helpful in detailed localization of the FSHD gene. Two of our families include males with a rapidly progressive muscle disease that had been diagnosed, on the basis of clinical features, as Duchenne muscular dystrophy. One of these males is available for linkage study and shares the haplotype of his FSHD-affected aunt and cousin.

Typing error is a major problem in constructing human linkage maps, leading to incorrect orders and inflating map lengths. An error filter is incorporated into multiple pairwise analysis that corrects for inflation of map lengths and improves recovery of the correct order. Multipoint mapping is more sensitive to error, but when its output is adjusted for both error and interference, map lengths are no longer inflated in proportion to the number of loci and are close to those obtained by multiple pairwise analysis.

Utilizing the CEPH reference panel and genotypic data for 53 markers, we have constructed a 20-locus multipoint genetic map of human chromosome 4. New RFLPs are reported for four loci. The map integrates a high-resolution genetic map of 4p16 into a continuous map extending to 4q31 and an unlinked cluster of three loci at 4q35. The 20 linked markers form a continuous linkage group of 152 cM in males and 202 cM in females. Likely genetic locations are provided for 25 polymorphic anonymous sequences and 28 gene-specific RFLPs. The map was constructed employing the LINKAGE and CRIMAP computational methodologies to build the multipoint map via a stepwise algorithm. A detailed 10-point map of the 4p16 region constructed from the CEPH panel provides evidence for heterogeneity in the linkage maps constructed from families segregating for Huntington disease (HD). It additionally provides evidence for position-specific recombination frequencies in the telomeric region of 4p.

The major limitation in performing predictive testing for Huntington disease (HD) is the unavailability of DNA from crucial family members. In our program approximately 20% (36/183) of persons have been excluded from predictive testing because of this reason. The major aim of this study was to examine whether data derived from linkage disequilibrium could modify risk analysis for persons at risk for HD. As a first step, we assessed whether the previously reported linkage disequilibrium between alleles recognized by probe pBS674E-D at locus D4S95 remained significant in a much larger data set. A total of 1,150 chromosomes from 622 individuals--200 affected and 422 unaffected--from 118 families were assessed. Significant haplotype association was detected with AccI and MboI RFLPs at the locus D4S95, with all the families (P = .00003), as well as for a subset from the United Kingdom (P = .0037). Data derived from linkage disequilibrium studies using D4S95 modifies the risk for HD, especially in persons of U.K. descent. Utilization of this approach for risk modification of HD awaits both validation of these data and additional information concerning ethnic-specific alleles at the D4S95 locus.

Nance-Horan Syndrome (NHS) or X-linked cataract-dental syndrome (MIM 302350) is a disease of unknown pathogenesis characterized by congenital cataracts and dental anomalies. We performed linkage analysis in three kindreds with NHS by using six RFLP markers between Xp11.3 and Xp22.3. Close linkage was found between NHS and polymorphic loci DXS43 (theta = 0 with lod score 2.89), DXS41 (theta = 0 with lod score 3.44), and DXS67 (theta = 0 with lod score 2.74), defined by probes pD2, p99-6, and pB24, respectively. Recombinations were found with the marker loci DXS84 (theta = .04 with lod score 4.13), DXS143 (theta = .06 with lod score 3.11) and DXS7 (theta = .09 with lod score 1.68). Multipoint linkage analysis determined the NHS locus to be linked completely to DXS41 (lod score = 7.07). Our linkage results, combined with analysis of Xp interstitial deletions, suggest that the NHS locus is located within or close to the Xp22.1-Xp22.2 region.

Van der Woude syndrome (VWS) is an autosomal dominant disorder in which affected individuals have one or more of the following manifestations: cleft lip, cleft palate, hypodontia, or paramedian lower-lip pits. VWS is a well-characterized example of a single-gene abnormality that disturbs normal craniofacial morphogenesis. As a first step in identifying genes involved in human development, we used a candidate-gene-and-region approach to look for a linkage to VWS. Six families with 3 or more generations of affected individuals were studied. Evidence for linkage (theta = 0.02, lod score = 9.09) was found between the renin (REN) gene on 1q and VWS. Other linked loci included CR1, D1S58, and D1S53. The genes for laminin B2 (LAMB2), a basement-membrane protein, and for decay-accelerating factor (DAF) were studied as possible candidate genes on 1q. Recombinants between VWS and both LAMB2 and DAF excluded these genes from a causal role in the etiology of VWS for the families studied in this report. Multipoint linkage analysis indicated that the VWS locus was flanked by REN and D1S65 at a lod score of 10.83. This tight linkage with renin and other nearby loci provides a first step in identifying the molecular abnormality underlying this disturbance of human development.

Börjeson-Forssman-Lehmann syndrome (BFLS) is a form of X-linked mental retardation (XLMR) with characteristic minor physical anomalies. It has no biochemical or cytogenetic markers. Heterozygous females may be entirely normal or may have mild-to-moderate manifestations. We studied 41 individuals from one family with BFLS for linkage on the X chromosome. The highest lod scores were 2.32 with DXS10 and 2.24 with DXS51, both at a theta = 0.0. A single recombinant was found between HPRT and BFLS. These results suggest that the BFLS locus is on the distal portion of Xq. Previously reported linkage studies in families with XLMR have not shown linkage with DXS10. This study suggests that one of the several X chromosome loci whose dysfunction is associated with mental retardation is located on distal Xq.

Using a cDNA for glycophorin A (MN), we screened 10 unrelated Caucasians using 22 restriction enzymes for RFLPs. A common StuI RFLP was identified and shown to be in marked linkage disequilibrium with both the MN and Ss blood-group antigens in a larger group of unrelated Caucasians. This provides a DNA marker for a locus that has been of major importance in genetic and population studies. The demonstrated disequilibrium will prove useful in localizing the gene for glycophorin B and in studies of genetic and physical distances on human chromosomes.

Strong linkage disequilibrium (LD) was found between DNA marker XV2c and the cystic fibrosis (CF) locus (delta = 0.46) and between DNA marker KM19 and CF (delta = 0.67) in 157 CF and 138 normal chromosomes from U.S. Caucasians. DNA haplotypes with nine polymorphic sites were created in 54 Caucasian families. There is a strong LD between the haplotypes and the presence of the mutant CF genes. This implies that the DNA polymorphisms examined are close to the CF gene and that one mutation of the CF gene predominates in the Caucasian population. Haplotype analysis can also be used to refine estimates of CF carrier risk in Caucasians. Data for XV2c and MET markers in 16 American black patients and their families revealed a different haplotype distribution and LD pattern with the CF locus. These data suggest that racial admixture alone does not explain the occurrence of CF in American blacks and that multiple alleles of the CF gene may exist in this population.

RFLPs for laminin B2 (LAMB2) are reported. These RFLPs were used to study the linkage relationships of LAMB2 to four other genes on lq: Duffy (FY), renin (REN), decay accelerating factor (DAF), and complement receptor 2 (CR2). Multipoint linkage analysis placed LAMB2 between FY and the cluster including REN, DAF, and CR2. This provides a useful bridging polymorphic marker on lq and establishes significant linkage of LAMB2 to FY (theta = 3.23, z = 3.85) and REN (theta = 0.17, z = 4.88).

A method is proposed to calculate the maximum likelihood estimate of gene frequency and linkage disequilibrium from disease-codominant marker conditional data. The method is illustrated using data on sickle-cell anemia and Duchenne muscular dystrophy and linked polymorphic restriction endonuclease cleavage sites.

Six restriction fragment length polymorphisms (RFLPs) detected in the human growth hormone-human chorionic somatomammotropin (hGH-hCS) gene cluster were studied in Mediterraneans, Northern Europeans, and American Blacks; the polymorphisms showed that, on the average, one of 500 bases in this cluster is variant. Haplotypes constructed for four of these RFLPs display strong nonrandom associations. However, the strongest associations were between RFLPs that are in homologous DNAs rather than between the physically closest RFLPs. From this and other evidence we argue that duplication of an ancestral hCS gene occurred at least twice, the second event being relatively recent. In other words, duplication of the hCS-L gene to produce the hCS-A gene occurred twice, so that hCS-A genes in humans may have independent origins. Our results imply that chromosomes with absent hCS genes (leading to hCS deficiency) may represent the nonduplicated ancestral unit rather than gene deletions.

New RFLPs are described for INP10 and interleukin 2. The 55 pairwise genetic linkage relationships for these two loci and nine additional loci on the long arm of chromosome 4 (4q) are reported. Fifteen new linkages are established, and new data are added to the four previously reported linkages on 4q. Tight linkage of interleukin 2 (T-cell growth factor), epidermal growth factor, and alcohol dehydrogenase is described. Significant differences were observed between male and female recombination rates. The female rate was estimated to be 1.27 times the male rate. On the basis of these pairwise results, the order for the 11 loci is D4S35-GC-(ALB/AFP)-MT2P1-D4S1-INP10-ADH3-( EGF/IL2)-(FBB/FBA/FBG)-MNS. This preliminary order can serve as a starting point for more detailed multipoint analysis.

Genetic linkage has been analyzed between cystic fibrosis (CF) and a number of markers on the long arm of chromosome 7, including D7S15, COL1A2, PON, MET, D7S8, and TCRB, using a cohort of 47 Canadian and 13 Danish CF families. The analysis confirms the previous observations that both MET and D7S8 are closely linked to CF. Based on the result from one family, MET appears to be more proximal to the centromere than CF. Our analysis also suggests that genetic heterogeneity may account for the high recombination fraction between CF and D7S8 observed in another family. In addition, a strong linkage disequilibrium has been observed between CF and the two closely flanking markers.

A strategy for using multiple linked markers for genetic counseling is to test sequentially individual markers until a diagnosis can be made. We show that in order to minimize the number of tests performed per case while diagnosing all informative cases the order in which the markers are to be tested is critical. We describe an algorithm to obtain this order using the parameter "I," the frequency of informative cases. The I value for a specific locus used depends on the marker frequency, association with the disease locus, and also on the informativeness of the marker loci already tested. Realizing that a direct assay for the beta S gene already exists, and that most cases of beta-thalassemia in Mediterraneans can be directly diagnosed using synthetic oligonucleotide probes, we illustrate the above technique by examining nine DNA polymorphisms in the human beta-globin cluster for their ability to diagnose sickle-cell anemia in American blacks and beta-thalassemia in Mediterraneans. This analysis shows that 95.39% of all sickle-cell pregnancies can be diagnosed by testing a subset of only six markers chosen by our algorithm. Furthermore, six markers can also diagnose 88.03% of beta-thalassemia in Greeks and 83.56% of beta-thalassemia in Italians. The test set is different from that suggested by the individual informative frequencies due to nonrandom associations between the restriction sites.