Brief introduction to human DNA fingerprinting

Shadows of doubt: the uneasy incorporation of identification science into legal determination of paternity in Brazil

The arrival of DNA paternity testing in the 1980s was met with great enthusiasm in the Brazilian courts. Yet, over the past two decades, Brazilian legal doctrine and jurisprudence have increasingly rejected DNA proof as the sine qua non for paternity cases. Instead, DNA paternity testing has generated mountains of litigation, as biological proof has been challenged by the argument that paternity is primarily “socio-affective”. Leading family law specialists describe this new conception of paternity as an outcome of the “revolutionary” provisions of the 1988 Constitution, which recognizes the “pluralism” of family forms in modern society and guarantees equal family rights for all children. Without denying the significance of the constitution’s dignitary framework, we show that new legal understandings of paternity represent less a paradigm shift than a continuation of longstanding historical tensions between biological and socio-cultural understandings of family and identity. In this article, we explore the development of biological and eventually genetic typing in Brazil, both of which had ties to the fields of criminology and race science. Our review suggests that techniques of biological identification, no matter how sophisticated or precise, were ineffective means for establishing identity, whether of individual personhood, as in the case of paternity, or national make-up. Instead, they became incorporated as supplemental methods into complex legal, social, and cultural decision-making around families.

Transposable elements are a significant contributor to tandem repeats in the human genome

Sequence repeats are an important phenomenon in the human genome, playing important roles in genomic alteration often with phenotypic consequences. The two major types of repeat elements in the human genome are tandem repeats (TRs) including microsatellites, minisatellites, and satellites and transposable elements (TEs). So far, very little has been known about the relationship between these two types of repeats. In this study, we identified TRs that are derived from TEs either based on sequence similarity or overlapping genomic positions. We then analyzed the distribution of these TRs among TE families/subfamilies. Our study shows that at least 7,276 TRs or 23% of all minisatellites/satellites is derived from TEs, contributing ∼0.32% of the human genome. TRs seem to be generated more likely from younger/more active TEs, and once initiated they are expanded with time via local duplication of the repeat units. The currently postulated mechanisms for origin of TRs can explain only 6% of all TE-derived TRs, indicating the presence of one or more yet to be identified mechanisms for the initiation of such repeats. Our result suggests that TEs are contributing to genome expansion and alteration not only by transposition but also by generating tandem repeats.

Unknown biological mixtures evaluation using STR analytical quantification

Allelic quantification of STRs, where the presence of three or more alleles represents mixtures, provides a novel method to identify mixtures from unknown biological sources. The allelic stutters resulting in slightly different repeat containing products during fragment amplification can be mistaken for true alleles complicating a simple approach to mixture analysis. An algorithm based on the array of estimated stutters from known samples was developed and tuned to maximize the identification of true non-mixtures through the analysis of three pentanucleotide STRs. Laboratory simulated scenarios of needle sharing generated 58 mixture and 38 non-mixture samples that were blinded for determining the number of alleles. Through developing and applying an algorithm that additively estimates stuttering around the two highest peaks, mixtures and non-mixtures were characterized with sensitivity of 77.5, 82.7 and 58% while maintaining the high specificity of 100, 97.4 and 100 for the W, X, and Z STRs individually. When all three STRs were used collectively, the resulting sensitivity and specificity was 91.4 and 97.4%, respectively. The newly validated approach of using multiple STRs as highly informative biomarkers in unknown sample mixture analyses has potential applications in genetics, forensic science, and epidemiological studies.

Somatic mutations at STR loci--a reason for three-allele pattern and mosaicism

Two families are analysed in which one of the parents exhibited a three-allele pattern at the ACTBP2 locus. Since the alleles were obviously segregated independently to the children, a generalised mosaicism must be assumed involving at least two tissues in one of them and at least four tissues in the other one. The intensity of the PCR amplified alleles in both three-allele individuals indicate an occurrence in a very early embryonic stage. Occurrence was most probably due to a single step mutation in both cases. Forensic implications would include paternity testing as well as stain analysis.

DNA profiling reveals remarkably low genetic variability in a herd of SLA homozygous pigs

Inbred strains of rodents have become indispensable for a wide range of biological studies. It has generally been accepted that genetic uniformity is unlikely to be achieved before 20 generations of brother x sister matings discouraging attempts to inbreed larger mammals. Nevertheless, pigs, homozygous for the swine MHC haplotype SLA b/b, have been inbred at the Babraham Institute for almost thirty years and used for immunological studies. Since the herd had not been studied at the DNA level, DNA profiling at multiple hypervariable loci was performed and surprisingly little genetic polymorphism and extremely high inter-individual resemblance were observed reminiscent of that observed in inbred strains of mice.

Human minisatellites, repeat DNA instability and meiotic recombination

Minisatellites include some of the most variable loci in the human genome and are superb for dissecting processes of tandem repeat DNA instability. Single DNA molecule analysis has revealed different mutation processes operating in the soma and germline. Low-level somatic instability results in simple intra-allelic rearrangements. In contrast, high frequency germline instability involves complex gene conversions and is therefore recombinational in nature, almost certainly occurring at meiosis. To determine whether true meiotic crossovers occur at human minisatellites, we have used polymorphisms near the repeat array to recover recombinant DNA molecules directly from sperm DNA. Analysis of minisatellite MS32 has revealed an intense and highly localised meiotic crossover hotspot centred upstream of the array, the first example of a human hotspot defined at the molecular level. This hotspot extends into the beginning of the repeat array, resulting in unequal and equal crossovers. Array crossovers occur much less frequently than array conversions but appear to arise by a common process, most likely by alternative processing of a recombination initiation complex. The location of MS32 at the boundary of a recombination hotspot suggests that this locus has evolved as a by-product of localised meiotic recombination activity, and that minisatellites might in general mark recombinationally proficient hotspots or hot domains in the genome. Finally, sperm crossover analysis makes it possible to explore the molecular rules that govern human meiotic recombination, and to detect phenomena such as meiotic drive that could provide a possible connection between recombination and DNA sequence diversity itself.

Utilization of microsatellites for the analysis of genomic alterations in colorectal cancers in Brazil

Two different pathogenetic mechanisms are proposed for colorectal cancers. One, the so-called "classic pathway", is the most common and depends on multiple additive mutational events (germline and/or somatic) in tumor suppressor genes and oncogenes, frequently involving chromosomal deletions in key genomic regions. Methodologically this pathway is recognizable by the phenomenon of loss of heterozygosity. On the other hand, the "mutator pathway" depends on early mutational loss of the mismatch repair system (germline and/or somatic) leading to accelerated accumulation of gene mutations in critical target genes and progression to malignancy. Methodologically this second pathway is recognizable by the phenomenon of microsatellite instability. The distinction between these pathways seems to be more than academic since there is evidence that the tumors emerging from the mutator pathway have a better prognosis. We report here a very simple methodology based on a set of tri-, tetra- and pentanucleotide repeat microsatellites allowing the simultaneous study of microsatellite instability and loss of heterozygosity which could allocate 70% of the colorectal tumors to the classic or the mutator pathway. The ease of execution of the methodology makes it suitable for routine clinical typing.

Mutation processes at human minisatellites

Minisatellites provide one of the most experimentally tractable systems for studying tandem repeat instability in man. Analysis of mutation processes has been greatly aided by the development of single molecule methods for recovering de novo mutants, and of techniques for exploring allele structure in detail. Application of these approaches to man has shown that minisatellites do not primarily mutate by processes such as replication slippage and unequal crossover intrinsic to the tandem repeat array. Instead, germline repeat instability is largely regulated by cis-acting elements near the array and involves unexpectedly complex processes of gene conversion, of potential relevance to the biology of meiosis. These processes can be explored both in humans and, in principle, in transgenic mouse models of human repeat instability.

Recent observations in human DNA-minisatellite mutations

We report maternal and paternal mutation rates at loci D1S7 (MS1), D7S21 (MS31), D12S11 (MS43A), and D7S22 (G3). The respective mutation rates were as follows: [table: see text] At loci D7S21, D12S11, and D7S22 statistically significant differences in mutation rates exist between the sexes. No such difference was observed at locus D1S7. However inspection of the latter data reveals that by mutation at spermiogenesis approximately two-thirds of the fragments showed an addition of repetitive units, while a 50: 50 ratio was encountered in the series of maternal mutations. We also report the observation of naturally occurring 3-fragment patterns.

Characterisation of a novel minisatellite that provides multiple splice donor sites in an interferon-induced transcript

Nucleotide sequence features of the human interferon-inducible gene 6-16 are described and include, within a CpG island, a partially expressed minisatellite consisting of 26 tandemly repeated dodecanucleotides. The repeat unit consensus sequence (CAGGTAAGGGTG) is similar to the mammalian splice donor consensus sequence [(A/C)AGGT(A/G)AGT]. The splice donor site of exon 2, as determined previously, forms part of the most upstream of the repeat units. We show that the two neighbouring repeat units also provide functional splice donor sites effectively extending exon 2 by 12 or 24 nt and inserting four or eight amino acids respectively into the predicted gene product. A similar pattern of differently spliced transcripts is detected in several human cell types. Both the number of repeat units per allele and the nucleotide sequence itself show limited polymorphism within the human population. Similar minisatellites from nonhuman primates are described and also appear to modulate splicing of a 6-16 transcript. The 6-16 minisatellite is therefore an example of tandemly repeated DNA that has a role in gene expression and may provide a useful in vivo system for the analysis of 5' splice site choice and minisatellite biology.