Identification of a unique Alu-based polymorphism and its use in human population studies

Alu elements represent a family of short interspersed DNA elements (SINEs) found in primate genomes. These are members of a group of transposable elements that integrate into the genome by the process of retrotransposition. Recent integrations of Alu elements within the human genome have generated presence/absence variants useful as DNA markers in human population studies as well as in forensic and paternity analyses. Besides the ease of use, this type of marker is unique because the absence of the Alu represents the ancestral form. We have identified an Alu-based polymorphism that consists of four alleles in which we can predict the evolutionary order. Additionally, we have developed a simple PCR plus restriction endonuclease assay to readily distinguish the four alleles. We have thus far analyzed DNA from a small set of samples comprising ten different ethnic groups. The three populations of African descent exhibited a relatively low frequency of the absence allele in contrast to the other populations, as well as being the only populations in which all four alleles were identified. One presence allele was not found in both European Caucasian and South American populations that were sampled, whereas a different presence allele was not observed among the sampled Asian populations. Additionally, the four-allele system identified variations among populations not observed by simply scoring as presence/absence variants. Therefore, extending beyond the two-allele dimorphic Alu system further elucidates population variations. These features afford this marker as a unique tool in the study of both global and regional analyses of human populations.     

Evolution of a human Y chromosome-specific repeated sequence

The structure and evolution of a repetitive sequence on the human Y chromosome has been studied by restriction enzyme analysis of both total DNA and the isolated sequence. The sequence is shown to cross-hybridize to sequences in female DNA forming unstable duplexes. Mouse/human cell hybrids have been used to investigate the pattern of sequence homology on the X chromosome and some autosomes. We conclude that this sequence is related to human satellite III, but shows considerable differences in structure.     

DNA polymorphism in a worldwide sample of human X chromosomes

DNA sequence data from humans can provide insight into the history of modern humans and the genetic variability in human populations. We report here a study of human DNA sequence variation at an X-linked noncoding region of 10,346 bp. The sample consists of 62 X chromosomes from Africa, Europe, and Asia. Forty-four polymorphic sites were found among the 62 sequences, resulting in 23 different haplotypes. Statistical analyses of the data led to the following inferences. (1) There is strong evidence of human population expansion in the relatively recent past, and this population expansion has had a significant effect on the pattern of polymorphism at this locus. (2) Non-African populations were unlikely to have been derived from a very small number of African lineages. (3) There was considerable geographic subdivision in the ancient human population, which could be an important reason why many studies failed to detect population expansion. (4) The long-term effective population size of humans is between 12,000 and 15,000. And (5) a non-African specific variant was found at a frequency of 35% in non-Africans, an estimate supported by the genotyping of additional 80 non-African and 106 African X chromosomes. This variant could have arisen in Eurasia more than 140,000 years ago, predating the emergence of modern humans. Moreover, this haplotype and all other haplotypes coalesced to the most recent common ancestor of the sample, which was estimated to be older than 490,000 years. Therefore, this region may have a long history in Eurasia.     

A chimpanzee-derived chromosome-specific alpha satellite DNA sequence conserved between chimpanzee and human

We describe a cloned 2.7 kb alpha satellite sequence, Pan-3, from the pygmy chimpanzee (Pan paniscus) that specifically hybridizes in situ to chromosome 19 in the pygmy chimpanzee and to the homeologous human chromosome, no. 17. Using high stringency conditions of hybridization on Southern blots, this sequence hybridized to DNA from both species of chimpanzee (P. paniscus and P. troglodytes) and from human but not to DNA from gorilla (Gorilla gorilla) or orangutan (Pongo pygmaeus). Partial sequence analysis showed that Pan-3 and a previously described human chromosome 17-specific clone have up to 91% sequence identity. To our knowledge this is the highest sequence similarity reported between alphoid subsets from human and any other primate.by T.C. Hsu     

The linkage information content value of polymorphism genetic markers in model-free linkage analysis

Guo and Elston [Hum Hered 1999;49:112-118] developed a linkage information content (LIC) value to measure the informativeness of a marker for identity-by-descent (IBD) sharing status of relative pairs. LIC values were derived for five types of relative pairs: full sib, half sib, grandparent-grandchild, first cousin and avuncular. In this paper, we give corrected LIC values for full sib, grandparent-grandchild, first cousin and avuncular pairs, and indicate the availability of a computer program to calculate them.     

Co-recessive inheritance: a model for DNA repair, genetic disease and carcinogenesis

A genetic model for some cases of excision-deficient xeroderma pigmentosum (XP) is proposed in which the trait (i.e., XP) is expressed if and only if the individual is homozygous or hemizygous for defective alleles at more than one of a specific set of loci. The model might also apply in some cases of certain other diseases associated with defective DNA repair. The model accounts for several paradoxical aspects of XP, including the large number of complementation groups despite the biochemically limited DNA-repair defect, the co-existence of XP and Cockayne's syndrome in two different complementation groups of XP, siblings with markedly different degrees of severity of XP in one family and transmission of the disease in an X-linked manner in another, the existence of some individuals who appear to have the DNA-repair defect but not clinical XP, and the seeming paradox of a disease associated with a marked defect in a DNA-repair mechanism but not associated with an obvious increase in incidence of internal cancer. The model predicts that a large proportion of the general population is a carrier of one or more of these defective genes for DNA-repair mechanisms. Such genes may be important in the etiology of much of human cancer.     

A chromosome-specific DNA sequence which reveals a high level of RFLP in wheat

Summary An unusual genomic DNA clone, PSR454, was isolated from a partial genomic library of wheat. This sequence is moderately repeated and detects at least 30 related sequences, all located in a tight linkage block on the long arm of chromosome 3B. When used as a RFLP probe, PSR454 detects a high level of polymorphism between wheat varieties that carry the sequence. There is no detectable hybridisation to sequences in one-third of the varieties tested, providing an on-off polymorphism that can be detected on dot blots, rather than the more resource-consuming conventional Southern analysis.     

Isolation of a human DNA sequence which spans the fragile X

To identify the sequences involved in the expression of the fragile X and to characterize the molecular basis of the genetic lesion, we have constructed yeast artificial chromosomes (YACs) containing human DNA and have screened them with cloned DNA probes which map close to the fragile site at Xq27.3. We have isolated and partly characterized a YAC containing approximately 270 kb of human DNA from an X chromosome which expresses the fragile X. This sequence in a yeast artificial ring chromosome, XTY26, hybridizes to the two closest DNA markers, VK16 and Do33, which flank the fragile site. The human DNA sequence in XTY26 also spans the fragile site on chromosome in situ hybridization. When a restriction map of XTY26, derived by using infrequently cutting restriction enzymes, is compared with similar YAC maps derived from non-fragile-X patients, no large-scale differences are observed. This YAC, XTY26, may enable (a) the fragile site to be fully characterized at the molecular level and (b) the pathogenetic basis of the fragile-X syndrome to be determined.     

Polymorphism in a human chromosome-specific interstitial telomere-like sequence at 22q11.2

Interstitial telomeric sequences (ITSs) are common in human. We previously reported the presence of an ITS at 22q11.2 which is in the vicinity of the genomically unstable region involved in 22q11 rearrangements. Recently, we studied the molecular status of the ITS 22q11.2 in the normal population. The amplification of an ITS at 22q11.2 showed different patterns ranging from 1-4 kb, confirming the highly polymorphic nature of this sequence. The linkage analysis of the ITS at 22q11.2 in members of 10 different families demonstrated a strong relation between offspring and parents. In contrast, the study of a DiGeorge case and his 2 parents revealed the presence of a novel allele probably inherited from the father. These results open an avenue for the use of this sequence as an allelic marker, and its implication in 22q11.2-related pathogenesis.     

Characterization of a human alphoid satellite DNA sequence: Potential use in assessing genetic diversity in Indian populations

Sequence analysis of a human repetitive DNA sequence (pTRF5.6) revealed considerable homology (76%) to the alphoid consensus sequence. Genomic blots of StuI-digested human DNA, hybridized to pTRF5.6, generated a ladder of bands with each band corresponding to oligodeoxyribonucleotide of an approx. 170-bp repeat, indicating a tandemly arrayed organization of this repeat element within the genome. Genomic hybridization analyses of unrelated individuals belonging to various geographical regions of India, using this alphoid satellite probe, revealed polymorphic bands ranging between 2 and 9 kb. Along with an individual-specific band pattern, several isomorphic bands below 2 kb were also evident. There was very little of genetic variability between populations, suggestive of low polymorphism at the inter-population level. Our result suggest that alphoid satellite sequence probe can be used in assessing the genetic diversity of various ethnic groups/populations belonging to different geographical regions.     

The use of chloroplast DNA polymorphism in studies of gene flow in plants

In many species of plants, the dispersal of genes is mediated by the movement of both seeds and pollen. The relative contributions of seed and pollen movement to total gene flow can be difficult to estimate. Chloroplast DNA (cpDNA) may prove useful for resolving this problem. Over the past several years, studies of numerous species of plants have shown that intraspecific variation in cpDNA is often sufficiently abundant to serve as a marker for studies of gene flow. Recent theoretical models have shown that estimates of population structure based on cpDNA polymorphism should be especially sensitive to the impact of seed movement on gene flow, because cpDNA is often maternally inherited.     

On the use of DNA fingerprints for linkage studies in cattle

To find a marker for the bovine "muscular hypertrophy" gene and for the "roan" locus, we have typed six cattle pedigrees totaling 540 animals for nine blood group systems, for 12 biochemical markers, for RFLPs at four loci, and with five probes revealing multilocus DNA fingerprints. Segregation analysis of the fingerprint bands showed that, in cattle, a fingerprint probe will reveal a mean of 7.6 clearly resolvable bands, behaving as simple, highly informative Mendelian entities characterized by a mean mutation rate of +/- 1/4500 gametes. For one of the bands, we observed a "mutation burst" generating germline mosaicism. Because some of the fingerprint bands were allelic or corresponded to clustered minisatellites, a mean of only 5.7 independent loci is explored per probe. Fingerprint bands revealed by different probes also show a clear propensity for close linkage, pointing toward nonrandom distribution of minisatellite sequences or the existence of minisatellite clusters. Although this reduces the power of fingerprints for linkage analysis substantially, we were able to demonstrate genetic linkage between fingerprint bands and at least three of the classical markers, to exclude the roan locus from 4.5 Morgans of the bovine genome with the DNA fingerprints and for an additional 2.5 Morgans with the classical markers, and to identify a solid candidate marker for the bovine muscular hypertrophy gene, yielding a lod score greater than or equal to 2.84 without any obliged recombinant.     

Close linkage between Norrie disease,a cloned DNA sequence from the proximal short arm,and the centromere of the X chromosome

Summary Norrie disease (ND) is an X-linked recessive disorder with congenital blindness (atrophia bulborum hereditaria, pseudoglioma). Six kindreds segregating for ND were studied for linkage with polymorphic markers of the human X chromosome. No recombination was observed between the ND-locus (NDP) and the DXS7 locus, the latter followed as a DNA-restriction fragment length polymorphism, detected by the recombinant DNA probe L1.28, and assigned to the region Xp11.2–Xp11.3. The maximum lod scores are at . Linkage data between NDP and the other genetic markers used in the present study are in keeping with this assignment of the mutation to the proximal Xp.     

The identification of a repeated DNA sequence involved in the karyotype polymorphism of the human Y chromosome

We show that individual men are polymorphic for the amount of two different repeated DNA sequences. The amount of one of these sequences is proportional to the length of the brightly fluorescent heterochromatin on the Y chromosome. There are no detectable alterations in sequence between polymorphic individuals. Female DNA contains sequences complementary to those found on the Y, but at a much reduced level.     

Radioresistant DNA synthesis and human genetic disease

Summary Sixty-eight human fibroblast cell strains were assayed for radioresistant DNA synthesis (RDS), which is defined here as the absence of a steep component of inhibition of DNA synthesis in a dose-response curve when rate of DNA synthesis is plotted against radation doses from 0 to 20 Gy or more. Twenty-seven strains from patients who were previously diagnosed to have ataxia-telangiectasia (AT) were positive for this feature. Among the cell strains that did not show RDS were two from AT obligate heterozygotes (i.e., the parents of AT patients), two from patients with Alzheimer disease, two from patients with Friedreich ataxia, one from a patient with Bloom syndrome, one from a patient with Down syndrome, and six from patients with various immunodeficiencies. Four strains demonstrated RDS that was less pronounced than in most AT cells: one was from a patient with Nijmegen breakage syndrome, one was from a patient without ataxia but with choreiform movement disorder, telangiectasia, and elevated concentrations of -fetoprotein in the blood, and two were from AT patients. RDS therefore is not a necessary trait of human genetic diseases that involve radiosensitivity or immunodeficiency. Although recent reports suggest that some AT patients do not exhibit RDS, we found RDS in all the AT cell we tested.     

The mechanism of maternal inheritance in Chlamydomonas: Biochemical and genetic studies

Summary The cytoplasmic linkage group of Chlamydomonas shows maternal inheritance, i.e. preferential transmission of cytogenes from the female (m t ⁺) parent and loss of the corresponding male (m t ^–) genome in sexual crosses. The mechanism of this process is postulated to be enzymatic modification of chloroplast DNA of the female to protect it from a restriction enzyme which degrades the chloroplast DNA of the male parent in the zygote soon after fusion. Genetic, biochemical and physical data bearing on this hypothesis are summarized and discussed.This paper is dedicated, with great admiration and affection, to Professor Marcus M. Rhoades, whose enthusiasm and curiosity contributed so much to my own scientific development, whose openness to biochemical and molecular interpretations of genetic data, played an exemplary role in focussing my own approach to research and whose fundamental studies of cytoplasmic inheritance in maize (Rhoades 1933, 1946) were directly responsible for my determination to tackle this difficult and perplexing area of research.     

The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat

A set of 20 wheat microsatellite markers was used with 55 elite wheat genotypes to examine their utility (1) in detecting DNA polymorphism, (2)in the identifying genotypes and (3) in estimating genetic diversity among wheat genotypes. The 55 elite genotypes of wheat used in this study originated in 29 countries representing six continents. A total of 155 alleles were detected at 21 loci using the above microsatellite primer pairs (only 1 primer amplified 2 loci; all other primers amplified 1 locus each). Of the 20 primers amplifying 21 loci, 17 primers and their corresponding 18 loci were assigned to 13 different chromosomes (6 chromosomes of the A genome, 5 chromosomes of the B genome and 2 chromosomes of the D genome). The number of alleles per locus ranged from 1 to 13, with an average of 7.4 alleles per locus. The values of average polymorphic information content (PIC) and the marker index (MI) for these markers were estimated to be 0.71 and 0.70, respectively. The (GT)_n microsatellites were found to be the most polymorphic. The genetic similarity (GS) coefficient for all possible 1485 pairs of genotypes ranged from 0.05 to 0.88 with an average of 0.23. The dendrogram, prepared on the basis of similarity matrix using the UPGMA algorithm, delineated the above genotypes into two major clusters (I and II), each with two subclusters (Ia, Ib and IIa, IIb). One of these subclusters (Ib) consisted of a solitary genotype (E3111) from Portugal, so that it was unique and diverse with respect to all other genotypes belonging to cluster I and placed in subcluster Ia. Using a set of only 12 primer pairs, we were able to distinguish a maximum of 48 of the above 55 wheat genotypes. The results demonstrate the utility of microsatellite markers for detecting polymorphism leading to genotype identification and for estimating genetic diversity. Received: 15 May 1999 / Accepted: 27 July 1999