The study of variation in the human genome

Indigenous Peoples, Postcolonial Contexts and Genomic Research in the Late 20th Century

In the 1960s the human geneticist James V. Neel and collaborators launched a research program aimed at investigating the human biology of South American indigenous populations, which would become one of the most influential such studies in the second half of the 20th century. In the first part of this article I explore the trajectory of some components of the Amazonian research program and situate it in the context of worldwide human biological research in the 1960s and 1970s. In the second half I suggest that the comparative analysis of previous research on the human biology of indigenous peoples might provide insights into highly debated issues pertaining to contemporaneous research agendas, including the `Human Genome Diversity Project' (HGDP).

A model-based 'varimax' sampling strategy for a heterogeneous population

BACKGROUND AND AIMS

Sampling strategies are planned to enhance the homogeneity of a sample, hence to minimize confounding errors. A sampling strategy was developed to minimize the variation within population groups. Karachi, the largest urban agglomeration in Pakistan, was used as a model population.

SUBJECTS AND METHODS

Blood groups ABO and Rh factor were determined for 3000 unrelated individuals selected through simple random sampling. Among them five population groups, namely Balochi, Muhajir, Pathan, Punjabi and Sindhi, based on paternal ethnicity were identified. An index was designed to measure the proportion of admixture at parental and grandparental levels. Population models based on index score were proposed. For validation, 175 individuals selected through stratified random sampling were genotyped for the three STR loci CSF1PO, TPOX and TH01.

RESULTS

ANOVA showed significant differences across the population groups for blood groups and STR loci distribution. Gene diversity was higher across the sub-population model than in the agglomerated population. At parental level gene diversities are significantly higher across No admixture models than Admixture models. At grandparental level the difference was not significant.

CONCLUSION

A sub-population model with no admixture at parental level was justified for sampling the heterogeneous population of Karachi.

Is urbanization scrambling the genetic structure of human populations? A case study

Recent population expansion and increased migration linked to urbanization are assumed to be eroding the genetic structure of human populations. We investigated change in population structure over three generations by analysing both demographic and mitochondrial DNA (mtDNA) data from a random sample of 2351 men from 22 Iranian populations. Potential changes in genetic diversity (theta) and genetic distance (F(ST)) over the last three generations were analysed by assigning mtDNA sequences to populations based on the individual's place of birth or that of their mother or grandmother. Despite the fact that several areas included cities of over one million inhabitants, we detected no change in genetic diversity, and only a small decrease in population structure, except in the capital city (Tehran), which was characterized by massive immigration, increased theta and a large decrease in F(ST) over time. Our results suggest that recent erosion of human population structure might not be as important as previously thought, except in some large conurbations, and this clearly has important implications for future sampling strategies.

Evidence for gradients of human genetic diversity within and among continents

Genetic variation in humans is sometimes described as being discontinuous among continents or among groups of individuals, and by some this has been interpreted as genetic support for "races." A recent study in which >350 microsatellites were studied in a global sample of humans showed that they could be grouped according to their continental origin, and this was widely interpreted as evidence for a discrete distribution of human genetic diversity. Here, we investigate how study design can influence such conclusions. Our results show that when individuals are sampled homogeneously from around the globe, the pattern seen is one of gradients of allele frequencies that extend over the entire world, rather than discrete clusters. Therefore, there is no reason to assume that major genetic discontinuities exist between different continents or "races."

Sequence Tag Catalogs of Dust Mite-Expressed Genomes

Dust mites are a major source of indoor allergens. They contain a large number of components that react with immunoglobulin (Ig) E in individuals with allergies and are capable of inducing sensitization, and allergic respiratory and cutaneous diseases. With a significant proportion of the population affected in some way by mite allergies, it is essential that we improve our understanding of these organisms so that control strategies could be defined and its allergens better understood. Thus, we have initiated a project using the expressed sequence tagging (EST) strategy to study the major species of dust mites associated with allergic diseases, in particular, the American house dust mite, Dermatophagoides farinae, as well as Blomia tropicalis, the most prevalent mite in domestic tropical dwellings. The work has recently been expanded to include 'storage' mites such as Tyrophagus putrescentiae, Acarus siro, Lepidoglyphus destructor, Glycyphagus domesticus, Suidasia medanensis, and Aleuroglyphus ovatus. More than 50% of the initial 3000 ESTs from the D. farinae and B. tropicalis dust mites showed significant matches to known genes and were categorized into eight functional groups (such as proteins involved in metabolism, gene expression, protein synthesis, cell signaling, etc.). Of specific interest, however, were the homologs to known mite allergens, in addition to a number of sequences bearing significant homology to allergens from non-mite sources previously not known to exist in mites. The availability of these allergen sequences has facilitated their expression and subsequent characterization in our laboratory in terms of their IgE-binding reactivity. The wealth of sequence information, generated via the EST project, has also facilitated the identification of polymorphic forms of allergens, the investigation of differential gene expression under various environmental conditions via DNA microarrays, as well as the analysis of protein level expression profiling via the proteomics approach. Additionally, ESTs have also ameliorated the understanding of the phylogenetic relationships between mites, and enabled the isolation of gene products crucial for life processes so that mite control strategies can be more effectively devised. Taken together, the utilization of the EST strategy has opened up numerous new avenues by which the allergist can engage more effectively in the study of dust mites with the ultimate aim of developing appropriate treatment regimens for mite-induced allergy.

Hierarchical patterns of global human Y-chromosome diversity

We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 males to study the geographic structure of Y-chromosome variation. Patterns of NRY diversity varied according to geographic region and method/level of comparison. For example, populations from Central Asia had the highest levels of heterozygosity, while African populations exhibited a higher level of mean pairwise differences among haplotypes. At the global level, 36% of the total variance of NRY haplotypes was attributable to differences among populations (i.e., Phi(ST) = 0.36). When a series of AMOVA analyses was performed on different groupings of the 50 populations, high levels of among-groups variance (Phi(CT)) were found between Africans, Native Americans, and a single group containing all 36 remaining populations. The same three population groupings formed distinct clusters in multidimensional scaling plots. A nested cladistic analysis (NCA) demonstrated that both population structure processes (recurrent gene flow restricted by isolation by distance and long-distance dispersals) and population history events (contiguous range expansions and long-distance colonizations) were instrumental in explaining this tripartite division of global NRY diversity. As in our previous analyses of smaller NRY data sets, the NCA detected a global contiguous range expansion out of Africa at the level of the total cladogram. Our new results support a general scenario in which, after an early out-of-Africa range expansion, global-scale patterns of NRY variation were mainly influenced by migrations out of Asia. Two other notable findings of the NCA were (1) Europe as a "receiver" of intercontinental signals primarily from Asia, and (2) the large number of intracontinental signals within Africa. Our AMOVA analyses also supported the hypothesis that patrilocality effects are evident at local and regional scales, rather than at intercontinental and global levels. Finally, our results underscore the importance of subdivision of the human paternal gene pool and imply that caution should be exercised when using models and experimental strategies based on the assumption of panmixia.

Genomic mismatch scanning identifies human genomic DNA shared identical by descent

Genomic mismatch scanning (GMS) is a high-throughput, high-resolution identity by descent mapping technique that enriches for genomic DNA fragments that are shared between related individuals. In GMS, DNA heteroduplexes are formed from restriction-digested genomic DNA fragments from two relatives. Mismatch-free DNA heteroduplexes, likely representing DNA shared identical by descent between the two individuals, are relatively purified by depleting the mismatch-containing heteroduplexes using the Escherichia coli mismatch repair proteins and exonuclease. Here, we demonstrate using quantitative microsatellite genotyping that, despite the complexity of the human genome, GMS can enrich the majority of restriction fragments that are identical by descent between two related humans. As the entire genome is selected in GMS, an extraordinarily dense set of markers (up to 200,000 markers) may be screened in parallel. The demonstration of the molecular enrichment of identical DNA fragments in the context of the whole human genome establishes conditions for the application of GMS to human genetics. This forms a frame-work for the further development of GMS as a hybridization-based mapping technique that utilizes DNA microarray technology to map the selected identical by descent DNA fragments.

TCOF1 gene encodes a putative nucleolar phosphoprotein that exhibits mutations in Treacher Collins Syndrome throughout its coding region

Treacher Collins Syndrome (TCS) is the most common of the human mandibulofacial dysostosis disorders. Recently, a partial TCOF1 cDNA was identified and shown to contain mutations in TCS families. Here we present the entire exon/intron genomic structure and the complete coding sequence of TCOF1. TCOF1 encodes a low complexity protein of 1,411 amino acids, whose predicted protein structure reveals repeated motifs that mirror the organization of its exons. These motifs are shared with nucleolar trafficking proteins in other species and are predicted to be highly phosphorylated by casein kinase. Consistent with this, the full-length TCOF1 protein sequence also contains putative nuclear and nucleolar localization signals. Throughout the open reading frame, we detected an additional eight mutations in TCS families and several polymorphisms. We postulate that TCS results from defects in a nucleolar trafficking protein that is critically required during human craniofacial development.

Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data

To test hypotheses about the origin of modern humans, we analyzed mtDNA sequences, 30 nuclear restriction-site polymorphisms (RSPs), and 30 tetranucleotide short tandem repeat (STR) polymorphisms in 243 Africans, Asians, and Europeans. An evolutionary tree based on mtDNA displays deep African branches, indicating greater genetic diversity for African populations. This finding, which is consistent with previous mtDNA analyses, has been interpreted as evidence for an African origin of modern humans. Both sets of nuclear polymorphisms, as well as a third set of trinucleotide polymorphisms, are highly consistent with one another but fail to show deep branches for African populations. These results, which represent the first direct comparison of mtDNA and nuclear genetic data in major continental populations, undermine the genetic evidence for an African origin of modern humans.

Genomic mismatch scanning: current progress and potential applications

Genomic mismatch scanning (GMS) is a new method of genetic mapping which attempts to purify and map the regions of identity between two complex genomes in a single test. Identical DNA fragments from two genomic sources are enriched in two steps: (i) after reannealing of the two genomes, heterohybrids are purified by using a combination of a restriction methylase and methylation-sensitive endonucleases, (ii) heterohybrids that contain mismatches are nicked in vitro by the E. coli MutHLS mismatch repair system and are eliminated subsequently from the pool, leaving only mismatch-free heterohybrids. The genomic origin of this selected pool of DNA fragments is then mapped in a single hybridization step onto metaphase chromosomes or ordered DNA arrays. The principal advantages of GMS are (i) it approaches the theoretical limit of mapping power and resolution offered by an arbitrarily dense set of completely informative polymorphic markers and (ii) it results in a great increase in the effective number of informative markers without a corresponding increase in the number of individual tests. Thus, it should provide an efficient method for affected-relative-pair linkage mapping and for linkage disequilibrium mapping. In addition, a variation of GMS may allow rapid genomic scanning for regions of homozygosity-by-descent or somatic loss-of-heterozygosity. The feasibility of GMS has been validated in the 15 mb genome of Saccharomyces cerevisiae. This article discusses the principles of GMS, the application to more complex genomes, and the possible uses of GMS.

Chromosomal localization and sequence analysis of a human episomal sequence with in vitro differentiating activity

The genomic fragment carrying the human activator of liver function, previously described as an episome capable of inducing differentiation upon transfection into a dedifferentiated rat hepatoma cell line, was mapped on human chromosome 12q24.2-12q24.3. This chromosomal location was indistinguishable by in situ hybridization from that of the gene coding for the hepatic transcription factor HNF1. The sequence of the integrated form of the episome as well as its flanking sequences show that it is rich in retroposons. It contains a human ribosomal protein L21 processed pseudogene, one truncated L1Hs sequence, and 10 Alu repeats, which belong to different subfamilies.

Identification of type I collagen gene polymorphisms: tolerance of sequence variation at an alpha 2(I) helix Y position

This study has examined the frequency and distribution of polymorphisms in the type I collagen coding sequences. RNA from a group of human skin fibroblast cell lines was analyzed by the chemical cleavage mismatch detection method using hydroxylamine, a reagent specific for C-base mismatches, and overlapping cDNA probes covering the entire prepro alpha 1(I) and prepro alpha 2(I) coding regions. Mismatches were detected at only two nucleotide positions, one in each of the type I collagen sequences, suggesting that polymorphisms are relatively rare within these cDNAs. cDNA sequence analysis demonstrated that the prepro alpha 1(I) mismatch, detected in only one cell line, was due to a sequence polymorphism involving the wobble position of the codon for arginine residue 59 within the amino-propeptide globular subdomain of the pro alpha 1(I) chain and not resulting in a change in the polypeptide primary structure. In contrast, the prepro alpha 2(I) mismatch, detected in 6 of the 16 cell lines, was shown to arise from a sequence polymorphism affecting the identity of Y-position residue 459 of the alpha 2(I) triple helical domain, resulting in an alanine/proline dimorphism at this position. This study is the first to identify a type I collagen coding sequence polymorphism resulting in an alteration at the level of the amino acid sequence. The data suggest that at least some alpha 1(I) and alpha 2(I) helix Y positions may be tolerant of sequence variation, particularly if the replacing amino acid is proline, a residue involved in stabilizing the collagen triple helix.

Comparison of human germ-line kappa gene sequences to sequence data from the literature

The question of which germ-line V kappa genes are expressed was studied by sequencing 70 different cDNA clones from a human spleen library and one clone from a fetal liver library. The sequences were compared to a data base containing all germ-line V kappa gene and pseudogene sequences. In addition, 51 rearranged genomic V kappa genes, 170 cDNA and 74 kappa proteins from the literature were assigned to specific germ-line V kappa genes and included in the comparisons. Not all the known, potentially functional V kappa genes were found to be expressed, while some genes with minor defects are. The total number of expressed genes is smaller than expected: so far 21 germ-line genes and 5 pairs of duplicated identical genes are known to be transcribed. The corresponding numbers for rearranged genomic V kappa genes and kappa proteins are 17 plus 4 and 7 plus 7, respectively. A second aim of the study was to find out whether the expressed repertoire contains derivatives of germ-line V kappa genes still missing in our data base; no evidence for the existence of such genes was found. Several cDNA clones contained additional nucleotides between the V kappa and J kappa gene segments, which may be germ-line derived, inserted by terminal deoxynucleotidyl transferase or introduced by other mechanisms. Somatic gene conversion seems not to play a major role in creating the human kappa gene diversity. Various aspects of the hypermutation of kappa genes are discussed and the formation of block mutations, i.e. the alterations of two or more adjacent nucleotides is stressed as a remarkable feature of the process.

Analysis of the promoter sequence and the transcription initiation site of the mouse 5-HT1C serotonin receptor gene

The serotonin 1c (5-HT1C) receptor is found in many brain regions, but is particularly enriched on the epithelial cells of the choroid plexus. A major challenge in neurobiology is to delineate the molecular processes that regulate the specific pattern of neuronal gene expression in the brain. As an initial step towards identifying cis-acting DNA sequences that control the expression of the 5-HT1C receptor, we have isolated the promoter sequence of its gene. Sequence analysis of a 1.8 kb fragment indicated that the 3' end of this fragment overlaps with the 5' untranslated region of the 5-HT1C receptor mRNA, and primer extension using mouse brain poly(A)+ RNA mapped the transcription initiation site within this fragment. There are a number of sequence elements upstream from the transcription initiation site that are homologous to regulatory elements found in other eucaryotic genes. To determine the promoter activity, a plasmid was constructed that contains this fragment as promoter region and the cDNA for the 5-HT1C receptor as the reporter. When injected into the nucleus of Xenopus oocytes, this construct resulted in functional expression of the reporter gene. Primer extension using the RNA extracted from the injected oocytes indicated a single transcription initiation site of the reporter mRNA. These results suggest that the 5-HT1C receptor was functionally expressed under the promoter activity of the 1.8 kb 5' sequence of its gene. This system will be useful for further analysis of the cis-acting elements in the promoter region of the 5-HT1C receptor gene and the trans-acting factors that regulate tissue-specific expression of the receptor.