Leonor Gusmão

Publication of population data for forensic purposes

In 2000 a new policy concerning the publication of population genetic data was set up in Forensic Science International [1] with the introduction of a new section entitled ‘‘Announcement of population data’’. The idea was to facilitate the publication of this type of data since the use of reliable allele or haplotype frequency estimates of the polymorphisms is a requirement in most countries, both in forensic and in paternity cases. Announcements of population data consisted in short communications under a fixed format, avoiding the repetition of superfluous information (i.e., materials and methods) and concentrating the message on the key information needed for the use of genetic data for forensic and population genetics. In our opinion, this type of paper completely fulfilled the aims of the editors and, even more importantly, has made an essential contribution to the dissemination of common standards all over the world. In addition they have motivated forensic practitioners (especially in countries with little development in forensic genetics) to introduce themselves in forensic research. With the launch of the new journal, we decided to continue the same policy as a first step but keeping in mind that we have to move forward to increase the quality of the journal and to avoid having a journal exclusively devoted to announcements of population genetic data. The number of population genetic papers from the very beginning has continuously increased, representing now more than 60% of the submissions to the journal. Therefore, it is time to raise the threshold regarding the acceptance of this type of publication but taking into account the importance of the dissemination of standards and the motivation that this type of research represents for some groups and countries. For this reason, we have decided to move to a next step and to introduce a new section on Forensic Population Genetics in the journal. Manuscripts with population genetic content can be submitted to this section at http://www.ees.elsevier.com/fsigen/ using three types of formats: Forensic Population Genetics – Original papers: in this section full length papers on relevant population genetics issues of forensic interest will be considered for publication. The data should be original, the population genetic analysis must be of the highest quality and the data should have forensic relevance beyond the scope of simply reporting allele or haplotype frequencies. Forensic Population Genetics – Short communications: understanding that both the quality of population data and the relevance of results are crucial, short communications will have the format of the former ‘‘Announcements of population data’’ with some changes (see below) in order to guarantee their quality.

Assessing individual interethnic admixture and population substructure using a 48–insertion‐deletion (INSEL) ancestry‐informative marker (AIM) panel

Estimating the proportions of different ancestries in admixed populations is very important in population genetics studies, and it is particularly important for detecting population substructure effects in case‐control association studies. In this work, a set of 48 ancestry‐informative insertion‐deletion polymorphisms (INDELs) were selected with the goal of efficiently measuring the proportions of three different ancestries (sub‐Saharan African, European, and Native American) in mixed populations. All selected markers can be easily analyzed via multiplex PCR and detected with standard capillary electrophoresis. A total of 593 unrelated individuals representative of European, African, and Native American parental populations were typed, as were 380 individuals from three Brazilian populations with known admixture patterns. As expected, the interethnic admixture estimates show that individuals from southern Brazil present an almost exclusively European ancestry; Afro‐descendant communities in the Amazon region, apart from the major African contribution, present some degree of admixture with Europeans and Native Americans; and a sample from Belém, in the northeastern Amazon, shows a significant contribution of the three ethnic groups, although with a greater European proportion. In summary, a panel of ancestry‐informative INDELs was optimized and proven to be a valuable tool for estimating individual and global ancestry proportions in admixed populations. The ability to accurately infer interethnic admixtures highlights the usefulness of this marker set for assessing population substructure in association studies, particularly those conducted in Brazilian and other Latin American populations sharing trihybrid ancestry patterns. Hum Mutat 31:184–190, 2010.

New guidelines for the publication of genetic population data.

In 2000 a new policy concerning the publication of population genetic data was set up in Forensic Science International [1] with the introduction of a new section entitled ‘‘Announcement of population data’’. Subsequently in 2010 [2] a new section on ‘‘Forensic Population Genetics’’ was introduced, and recommendations were redefined. FSI: Genetics is one of the few journals still considering population genetic data for publication and we strongly believe that this policy has contributed to the dissemination of common standards in the field all over the world and also to motivate labs and people to embark in research in the area of forensic genetics. For this reason it is our intention to continue with this policy, and recently an associate editor exclusively devoted to this topic was appointed to the journal. Despite having defined a more detailed procedure for acceptance, our journal is still receiving a massive number of submissions of varying quality in this area. Therefore it has become necessary to raise the threshold regarding the acceptance of this type of publication to ensure a high standard of published data. In addition we want to improve the submission, reviewing and publication procedures, and to correct some aspects that we have detected such as the obligation to meet ethical standards in the collection of samples including informed consent and approval by ethical committees. For this reason, we have decided to publish new guidelines for the publication of population genetic data in the journal.

A new multiplex for human identification using insertion/deletion polymorphisms.

Human identification is usually based on the study of STRs or SNPs depending on the particular characteristics of the investigation. However, other types of genetic variation such as insertion/deletion polymorphisms (indels) have considerable potential in the field of identification, since they can combine the desirable characteristics of both STRs and SNPs. In this study, a set of 38 non‐coding bi‐allelic autosomal indels reported to be polymorphic in African, European, and Asian populations were selected. We developed a sensitive genotyping assay, which is able to characterize all 38 bi‐allelic markers using a single multiplex PCR and detected with standard CE analyzers. Amplicon length was designed to be shorter than 160 bp. Complete profiles were obtained using 0.3 ng of DNA, and full genotyping of degraded samples was possible in cases where standard STR typing had partially failed. A total of 306 individuals from Angola, Mozambique, Portugal, Macau, and Taiwan were studied and population data are presented. All indels were polymorphic in the three population groups studied and the random match probabilities of the set ranged in orders of magnitude from 10−14 to 10−15. Therefore, the indel‐plex represents a valuable approach in human identification studies, especially in challenging DNA cases, as a more straightforward and efficient alternative to SNP typing.

Update of the guidelines for the publication of genetic population data

Due to the massive number of submissions of varying quality with population genetic data we decided one year ago to raise the threshold regarding the acceptance of this type of publications to ensure a high standard of published data and, therefore, we updated the FSI: Genetics 2010 guidelines [1] to a new set of recommendations [2]. In the 2013 guidelines in addition to some new requirements in the procedure and regarding ethical standards, we significantly increased the number of markers and samples required for submission to the journal of papers presenting population data alone, with no additional information on new methods or other forensically relevant findings. We have been working during last year with these new recommendations. During this period, we have received a number of critical comments from authors that we have considered and therefore we have decided to make some amendments in the requirements. The first change refers to the minimal number of autosomal STRs. The 2013 guidelines indicate that for data comprising autosomal STR genotypes only, 17 different autosomal STR loci are required as a minimum. This was based on the average number of STRs that most laboratories are routinely using – in most cases forensic laboratories are using at least two PCR multiplexes (commercial kits or homemade) on their routine work for a minimal number of 17 autosomal STR markers. However, this number would exclude laboratories and national and international compilation efforts that are working with just one kit, for some of the most commonly used kits. Whilst we certainly recognize the need to restrict the number of small data sets submitted we think that the forensic community would benefit from the publication of a large and nationally important data set such as the ones that are being generated in some countries. For this reason we have decided to reinstate the 2010 recommendations requiring 15 STRs only. Concerning X chromosome a minimum number of 12 STRs will be required and for the Y chromosome a minimum of 17 STRs will be required as well, taking into account that the core minimum haplotype (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385) [3,4] must be provided if it has not been previously analyzed in the same population sample. Collaborative efforts to produce large datasets are strongly encouraged and, therefore, the minimal number of markers should not be a limitation to the publication of large National or International collaborative databasing efforts when a significant number of laboratories and samples are involved. There are also changes in the requirements for the minimum number of samples. We maintain the threshold of 500 samples for

DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis

The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. A previous recommendation published in 2001 has already addressed Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). Since then, the use of Y-STRs has become very popular, and numerous new loci have been introduced. The current recommendations address important aspects to clarify problems regarding the nomenclature, the definition of loci and alleles, population genetics and reporting methods.

The genetic legacy of western Bantu migrations

There is little knowledge on the demographic impact of the western wave of the Bantu expansion. Only some predictions could be made based mainly on indirect archaeological, linguistic, and genetic evidences. Apart from the very limited available data on the mitochondrial DNA (mtDNA) side, there are not, however, Y-chromosome studies revealing–if any–the male contribution of western Bantu-farmers. To elucidate the still poorly characterized western Bantu expansion, we analyzed Y-chromosome (25 biallelic polymorphisms and 15 microsatellite markers) and mtDNA (hypervariable control regions I and II and selected coding region RFLPs) variation in a population of 110 individuals from southwest Africa, and compared it with a database of 2,708 Y-chromosome profiles and of 2,565 mtDNAs from all other regions of Africa. This study reveals (1) a dramatic displacement of male and female Khoisan-speaking groups in the southwest, since both the maternal and the paternal genetic pools were composed exclusively by types carried by Bantu-speakers; (2) a clear bias in the admixture process towards the mating of male Europeans with female Sub-Saharan Africans; (3) the assimilation of east African lineages by the southwest (mainly mtDNA-L3f and Y-chromosome-B2a lineages); and (4) signatures of recent male and female gene flow from the southeast into the southwest. The data also indicate that the western stream of the Bantu expansion was a more gradual process than the eastern counterpart, which likely involved multiple short dispersals.

ISFG: Recommendations regarding the use of non-human (animal) DNA in forensic genetic investigations

The use of non-human DNA typing in forensic science investigations, and specifically that from animal DNA, is ever increasing. The term animal DNA in this document refers to animal species encountered in a forensic science examination but does not include human DNA. Non-human DNA may either be: the trade and possession of a species, or products derived from a species, which is contrary to legislation; as evidence where the crime is against a person or property; instances of animal cruelty; or where the animal is the offender. The first instance is addressed by determining the species present, and the other scenarios can often be addressed by assigning a DNA sample to a particular individual organism. Currently there is little standardization of methodologies used in the forensic analysis of animal DNA or in reporting styles. The recommendations in this document relate specifically to animal DNA that is integral to a forensic science investigation and are not relevant to the breeding of animals for commercial purposes. This DNA commission was formed out of discussions at the International Society for Forensic Genetics 23rd Congress in Buenos Aires to outline recommendations on the use of non-human DNA in a forensic science investigation. Due to the scope of non-human DNA typing that is possible, the remit of this commission is confined to animal DNA typing only.

New Microsatellite Multiplex PCR for Candida albicans Strain Typing Reveals Microevolutionary Changes

ABSTRACT Five new microsatellite loci were described and characterized for use as molecular markers for the identification and genetic differentiation of Candida albicans strains. Following the typing of 72 unrelated clinical isolates, the analysis revealed that they were all polymorphic, presenting from 5 to 30 alleles and 8 to 46 different genotypes. The discriminatory power obtained by combining the information generated by three microsatellites used in a multiplex PCR amplification strategy was 0.99, the highest ever reported. The multiplex PCR was later used to test a total of 114 C. albicans strains, including multiple isolates from the same patient collected from different body locations and along episodes of vulvovaginal infections. Three different scenarios for strain relatedness were identified: (i) different isolates that were revealed to be the same strain, (ii) isolates that were the same strain but that apparently underwent a process of microevolution, and (iii) isolates that corresponded to different strains. Analysis of the microevolutionary changes between isolates from recurrent infections indicated that the genotype alterations observed could be the result of events that lead to the loss of heterozygosity (LOH). In one case of recurrent infection, LOH was observed at the CAI locus, and this could have been related to exposure to fluconazole, since such strains were exposed to this antifungal during treatment. The analysis of microsatellites by a multiplex PCR strategy was found to be a highly efficient tool for the rapid and accurate differentiation of C. albicans strains and adequate for the identification of fine microevolutionary events that could be related to strain microevolution in response to environmental stress conditions.

A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations

In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), a polymerase chain reaction multiplex was optimized in order to type ten X-chromosome short tandem repeats (STRs) in a single reaction, including: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08, and DXS7423. Using this X-decaplex, each 17 of the participating laboratories typed a population sample of approximately 200 unrelated individuals (100 males and 100 females). In this work, we report the allele frequencies for the ten X-STRs in 15 samples from Argentina (Buenos Aires, Córdoba, Río Negro, Entre Ríos, and Misiones), Brazil (São Paulo, Rio de Janeiro, Paraná, and Mato Grosso do Sul), Colombia (Antioquia), Costa Rica, Portugal (Northern and Central regions), and Spain (Galicia and Cantabria). Gene diversities were calculated for the ten markers in each population and all values were above 56%. The average diversity per locus varied between 66%, for DXS7133, and 82%, for DXS6809. For this set of STRs, a high discrimination power was obtained in all populations, both in males (≥1 in 5 × 105) and females (≥1 in 3 × 109), as well as high mean exclusion chance in father/daughter duos (≥99.953%) and in father/mother/daughter trios (≥99.999%). Genetic distance analysis showed no significant differences between northern and central Portugal or between the two Spanish samples from Galicia and Cantabria. Inside Brazil, significant differences were found between Rio de Janeiro and the other three populations, as well as between São Paulo and Paraná. For the five Argentinean samples, significant distances were only observed when comparing Misiones with Entre Ríos and with Río Negro, the only two samples that do not differ significantly from Costa Rica. Antioquia differed from all other samples, except the one from Río Negro.