Faculty Bibliography

With the advent of the Human Genome Project, the ability to rapidly construct comprehensive and accurate linkage maps based on genetic marker data from family studies is an absolute necessity. In addition to their usefulness in localizing genes for both simple and complex disorders, linkage maps are invaluable tools for genetic counseling using linked marker genes. Several computer program packages are publicly available which aid in the construction of linkage maps by computing multipoint likelihoods for specified locus orders. However, these programs work in a step-by-step fashion, requiring intensive user-intervention and analysis at each step. Such a repetitive process is amenable to computerized automation. We have developed and tested an expert system computer program, MultiMap, for automated genetic linkage mapping. This program greatly reduces the amount of user-computer interaction, increasing the accuracy and speed with which a map can be constructed. In addition, because the total mapping time is greatly reduced through automation, it is now feasible to explore and compare various mapping heuristics and mapping criteria in order to develop the most appropriate approach, or set of approaches, for genetic linkage mapping. MultiMap need not be restricted to the construction of genetic maps, but could be adapted to aid in the automated construction of physical maps as well.

We report the cloning, sequencing, and mapping of three short sequence repeat polymorphisms due to tetranucleotide (TAAA)n repeats from human chromosome 21. These DNA markers (D21S221, D21S225, D21S226) have been cloned from the chromosome 21-specific plasmid library of J. C. Fuscoe, C. C. Collins, D. Pinkel, and J. W. Gray (1989, Genomics 5: 100-109) and were shown to be polymorphic by polymerase chain reaction amplification and polyacrylamide gel electrophoresis. Genotypes were determined in informative CEPH pedigrees and used in linkage analysis relative to other mapped markers on human chromosome 21. One of these markers, D21S221, is closely linked to the amyloid precursor protein gene (APP), which has been implicated in the etiology of familial Alzheimer disease in some families.

To further develop the linkage map of human chromosome 21 (HC21), we have concentrated on identifying highly polymorphic markers based on dinucleotide repeat sequences such as (GT)n, as these are often highly polymorphic, are widespread throughout the human genome, and can be rapidly analyzed by the polymerase chain reaction. We report here nine (GT)n polymorphic markers from HC21.

A genetic linkage map of the human genome was constructed that consists of 1416 loci, including 279 genes and expressed sequences. The loci are represented by 1676 polymorphic systems genotyped with the CEPH reference pedigree resource. A total of 339 microsatellite repeat markers assayed by PCR are contained within the map, and of the 351 markers with heterozygosities of at least 70%, 205 are microsatellites. Seven telomere loci define physical and genetic endpoints for 2q, 4p, 7q, 8p, 14q, 16p, and 16q, and in other cases distal markers on the maps have been localized to terminal cytogenetic bands. Therefore, at least 92% of the autosomal length of the genome and 95% of the X chromosome is estimated to be spanned by the map. Since the maps have relatively high marker density and numerous highly informative loci, they can be used to map disease phenotypes, even for those with limited pedigree resources. The baseline map provides a foundation for achieving continuity of clone-based physical maps and for the development of a truly integrated physical, genetic, and cytogenetic map of the human.

We have detected a polymorphism in the 3' untranslated region of the AML1 gene, which is located at the breakpoint on chromosome 21 in the t(8;21)(q22;q22.3) translocation often associated with patients with acute myeloid leukemia. Informative CEPH families were genotyped for this polymorphism and used to localize the gene on the linkage map of human chromosome 21. The AML1 gene is located between the markers D21S216 and D21S211, in chromosomal band 21q22.3.

A genetic case-control study was conducted in a group of patients with schizophrenia (n = 67; DSM-III) and psychiatrically normal controls matched for ethnicity (n = 84), living in the same geographical area. Using three different DNA polymorphisms of the gene encoding porphobilinogen deaminase (PBGD), a candidate gene for schizophrenia, an association with schizophrenia could not be detected. No significant associations were detected even after sub-division of the cohort by ethnicity and by gender.

Nondisjunction in trisomy 21 has traditionally been studied by cytogenetic heteromorphisms. Those studies assumed no crossing-over on the short arm of chromosome 21. Recently, increased accuracy of detection of the origin of nondisjunction has been demonstrated by DNA polymorphism analysis. We describe a comparative study of cytogenetic heteromorphisms and seven PCR-based DNA polymorphisms for detecting the origin of the additional chromosome 21 in 68 cases of Down syndrome. The polymorphisms studied were the highly informative microsatellites at loci D21S215, D21S120, D21S192, IFNAR, D21S156, HMG14, and D21S171. The meiotic stage of nondisjunction was assigned on the basis of the pericentromeric markers D21S215, D21S120, and D21S192. Only unequivocal cytogenetic results were compared with the results of the DNA analysis. The parental and meiotic division origin could be determined in 51% of the cases by using the cytogenetic markers and in 88% of the cases by using the DNA markers. Although there were no discrepancies between the two scoring systems regarding parental origin, there were eight discrepancies regarding meiotic stage of nondisjunction. Our results raise the possibility of recombination between the two marker systems, particularly on the short arm.

A plasmid, AWZ1, that contained a dinucleotide (GT)n repeat was identified from a chromosome 21-specific genomic library. When amplified by PCR from human genomic DNA, the repeat length was highly polymorphic between individuals; its location, D21S215, was mapped in the CEPH pedigrees by linkage analysis to the pericentromeric region of chromosome 21. It is the closest polymorphic marker to alphoid sequences on this chromosome.

This report presents cytogenetic data on three cases of malignant ovarian germ cell tumors. All were diagnosed as malignant teratoma; case 1 with yolk sac elements; case 2 with elements of endodermal sinus tumor, embryonal carcinoma, and choriocarcinoma; and case 3 with yolk sac elements and embryonal carcinoma. Metaphase cells from each tumor, and normal tissue from the host, were karyotyped and scored for centromeric heteromorphisms in an attempt to determine the mechanism of origin. The karyotypes were 79,XXX,+1,+3,-6,+8,+12,+14,-15,+17, +20,+21,+22;49,XX,+8,+12,+22; and 48,XX,+3,+14, respectively. The analysis of centromeric heteromorphisms and DNA fingerprints of host and teratoma using the M13 probe revealed that one case originated from a germ cell before the first meiotic division. Normal host tissue was not available in case 2, but several centromeric markers were heterozygous in the tumor, indicating either meiosis I error or complete failure of germ cell meiosis. In the third case the centromeric heteromorphisms that were heterozygous in the host appeared to be homozygous for certain chromosomes and heterozygous for others in the tumor. These results suggest that germ cell teratomas could arise by the fusion of two ova.