Haplotype diversity in mitochondrial DNA hypervariable region in a population of southeastern Brazil

Genetic characterisation of the North-West Indian populations: analysis of mitochondrial DNA control region variations

BACKGROUND

Human mitochondrial DNA presents several interesting characteristics, making it a favourable tool in the field of molecular anthropology, medical genetics, population history, and forensic science.

AIM

The present study investigated the mitochondrial DNA (mtDNA) control region variations in diverse ethnic groups of North-West India for which population data is insufficient.

SUBJECTS AND METHODS

The complete mtDNA control regions of 197 unrelated (for up to three generations) healthy individuals belonging to different ethnic groups of North-West India were sequenced. The haplotype frequencies, haplogroup distribution, and pairwise F_ST values between the studied and other worldwide populations were generated to study patterns of variation in human mtDNA.

RESULTS

The results ascertained high gene diversity (0.998) in the studied maternal lineages, identifying 166 distinct haplotypes, of which 158 were unique and characterised by 117 variable sites. Three haplogroups: M3, M30, and U7 were observed to be the most prevalent, and phylogeographically a total of 55.86% of sequences were characterised into South Asian, followed by West Eurasian (40.18%) and East Asian (3.96%), ancestry haplogroups. Pairwise genetic differentiation comparisons revealed maternal homogeneity in the studied groups. No population substructure was detected within the North-West Indian populations.

CONCLUSION

The results of this preliminary study will contribute to an existing database of mtDNA variations of the Indian population and facilitate prospective studies investigating population genetics and human diseases.

Developmental validation of the MGIEasy Signature Identification Library Prep Kit, an all-in-one multiplex system for forensic applications

Analyzing genetic markers in nuclear and mitochondrial genomes is helpful in various forensic applications, such as individual identifications and kinship analyses. However, most commercial kits detect these markers separately, which is time-consuming, laborious, and more error-prone (mislabelling, contamination, ...). The MGIEasy Signature Identification Library Prep Kit (hereinafter "MGIEasy identification system"; MGI Tech, Shenzhen, China) has been designed to provide a simple, fast, and robust way to detect appropriate markers in one multiplex PCR reaction: 52 autosomal STRs, 27 X-chromosomal STRs, 48 Y-chromosomal STRs, 145 identity-informative SNPs, 53 ancestry-informative SNPs, 29 phenotype-informative SNPs, and the hypervariable regions of mitochondrial DNA (mtDNA). Here, we validated the performance of MGIEasy identification system following the guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM), assessing species specificity, sensitivity, mixture identification, stability under non-optimal conditions (degraded samples, inhibitor contamination, and various substrates), repeatability, and concordance. Libraries prepared using MGIEasy identification system were sequenced on a MGISEQ-2000 instrument (MGI Tech). MGIEasy-derived STR, SNP, and mtDNA genotypes were highly concordant with CE-based STR genotypes (99.79%), MiSeq FGx-based SNP genotypes (99.78%), and Sanger-based mtDNA genotypes (100%), respectively. This system was strongly human-specific, resistant to four common PCR inhibitors, and reliably amplified both low quantities of DNA (as low as 0.125 ng) and degraded DNA (~ 150 nt). Most of the unique alleles from the minor contributor were detected in 1:10 male-female and male-male mixtures; some minor Y-STR alleles were even detected in 1:1000 male-female mixtures. MGIEasy also successfully directly amplified markers from blood stains on FTA cards, filter papers, and swabs. Thus, our results demonstrated that MGIEasy identification system was suitable for use in forensic analyses due to its robust and reliable performance on samples of varying quality and quantity.

Etiology of intellectual disability in individuals from special education schools in the south of Brazil

Background

Intellectual Disability (ID) is characterized by significant limitations that affect intellectual functioning, adaptive behavior, and practical skills which directly interfere with interpersonal relationships and the environment. In Western countries, individuals with ID are overrepresented in the health system, often due to associated comorbidities, and its life-time cost places ID as one of the most expensive conditions of all diagnoses in the International Classification of Diseases. Most of the people affected (75%) live in low-income countries, suffer from malnutrition, lack health care, and do not have access to adequate treatment. The aim of this study was to obtain an estimate of the diagnostic status as well as the prevalence of familial ID among individuals with serious (moderate or severe) ID in a region of the State of Santa Catarina, investigating attendees of special education schools of the Florianópolis Macroregion.

Methods

This was a cross-sectional study conducted between August 2011 and August 2014, through a semi-structured screening questionnaire for the collection of relevant developmental, clinical, familial and educational data, applied in an interview to guardians of students of special education schools of the macroregion of Florianópolis.

Results

The participant special schools enrolled close to 1700 students during the study period and the questionnaire was applied to 849 (50.5%). The male to female ratio of the participants was 1.39:1. Clear etiologic explanations were relatively scarce (24%); most diagnoses referring only to the type and the degree of impairment and for the majority (61.4%) the cause was unknown. About half were sporadic cases within their families (considering three generations). For 44.2% at least one other case of an ID-related condition in the extended family was mentioned, with 293 (34.5%) representing potential familial cases.

Conclusion

Here we describe the epidemiological profile, the available diagnostics, etiology, family history and possible parental consanguinity of participants with ID of special education schools in the South of Brazil. The main results show the need for etiological diagnosis and uncover the relevance of potential hereditary cases in a population where consanguineous unions have a relatively low frequency (0,6%) and highlight the need for public health actions.

Supplementary information

Supplementary information accompanies this paper at 10.1186/s12887-020-02382-5.

Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods

The use of Massive Parallel Sequencing (MPS) techniques have been proposed by the forensic community as an alternative to Sanger sequencing methods in routine forensic casework analysis regarding mitochondrial DNA (mtDNA). Interesting features of MPS include high throughput, ability to simultaneously genotype a significant number of samples by barcoding techniques, processing automation, reduced time and costs, among others. Advantages include the capability of generating full mtDNA genome sequences versus usual techniques, usually limited to hypervariable or control regions exclusively. In this work, 96 reference single-source samples from three different Brazilian cities were subjected to full mtDNA genome sequencing by MPS techniques using an early-access version of Precision ID mtDNA Whole Genome Panel on an Ion Torrent PGM platform (Thermo Fisher Scientific, Waltham, MA, USA). Complete, high-quality sequences were obtained and sequencing performance was evaluated via four different metrics. As a subset of evaluated samples have been previously submitted for Sanger sequencing of the control region, a comparative analysis of both methods' results was conducted in order to compare technique adequacy within a forensic context. Even though this study is one of the first to report full mtDNA genome sequences for Brazilian admixed populations, the observed haplotypes exhibit a predominance of Native American and African maternal lineages in the studied sample set, reproducing results described in the literature for control regions only. Interpopulation analysis among Brazilian and 26 worldwide populations was also carried out. The results indicate that MPS-generated full mtDNA genome sequences may have great utility in forensic real casework applications, with a pronounced gain of genetic information and discrimination power provided by coding region evaluation and the enhanced capacity of heteroplasmies determination. Database construction and other relevant factors concerning implementation of such techniques in Brazilian forensic laboratories are also discussed.

Mitochondrial DNA control region haplotypes and haplogroup diversity in a sample from Brasília, Federal District, Brazil

Brazilians form one of the most heterogeneous populations in the world, as the result of five centuries of miscegenation between its native populations with migrants from Europe, Africa and Asia. The present study intended to characterize the frequencies of mtDNA haplotypes in a dataset of 306 individuals from Brasília, Federal District of Brazil. Brasília was built from scratch in the late 1950s and its construction attracted migrants from different regions of Brazil, mostly from Central-West, Northeast and Southeast regions. Due to its formation, its population is admixed. The goal of this study was to collect mtDNA population data and contribute to databases for a better use of mtDNA for forensic purposes. The haplotypes are available at EMPOP website under accession number EMP00695.

Mitochondrial DNA control region diversity in a population from Parana state-increasing the Brazilian forensic database

The entire mitochondrial DNA (mtDNA) control region (nucleotide position 16024-576) sequences were obtained through Sanger sequencing method for 122 individuals from Parana state, South of Brazil. We observed a total of 108 different haplotypes of which 97 were unique and 11 were shared by more than one individual. The haplogroups were classified according to the updated mtDNA phylogeny, by EMMA (estimating mitochondrial haplogroups using a maximum likelihood approach). Our results revealed the predominance of Amerindian haplogroups with a frequency of 49.2% of the population sample, followed by European lineages with 38.5% and 12.3% of African lineages. Parana population sample set presented a high haplotype diversity (0.9976) and the random match probability was 0.0106. The phylogenetical findings and the diversity indices confirm the high genetic heterogeneity of this population and suggest a high informativeness of mtDNA analyses in forensic cases. The population data will contribute to increase the Brazilian mtDNA database for forensic purposes and it is available through EMPOP (European DNA Profiling Group mitochondrial DNA population database) under the accession number EMP00714.

Defining mtDNA origins and population stratification in Rio de Janeiro

The genetic composition of the Brazilian population was shaped by interethnic admixture between autochthonous Native Americans, Europeans settlers and African slaves. This structure, characteristic of most American populations, implies the need for large population forensic databases to capture the high diversity that is usually associated with admixed populations. In the present work, we sequenced the control region of mitochondrial DNA from 205 non-related individuals living in the Rio de Janeiro metropolitan region. Overall high haplotype diversity (0.9994 ± 0.0006) was observed, and pairwise comparisons showed a high proportion of haplotype pairs with more than one-point differences. When ignoring homopolymeric tracts, pairwise comparisons showed no differences 0.18% of the time, and differences in a single position were found with a frequency of 0.32%. A high percentage of African mtDNA was found (42%), with lineages showing a major South West origin. For the West Eurasian and Native American haplogroups (representing 32% and 26%, respectively) it was not possible to evaluate a clear geographic or linguistic affiliation. When grouping the mtDNA lineages according to their continental origin (Native American, European and African), differences were observed for the ancestry proportions estimated with autosomal ancestry-informative markers, suggesting some level of genetic substructure. The results from this study are in accordance with historical data where admixture processes are confirmed with a strong maternal contribution of African maternal ancestry and a relevant contribution of Native American maternal ancestry. Moreover, the evidence for some degree of association between mtDNA and autosomal information should be considered when combining these types of markers in forensic analysis.

Polymorphisms of mitochondrial DNA control region are associated to endometriosis

PURPOSE

Polymorphisms in the control region of mitochondrial DNA (mtDNA) can affect generation of reactive oxygen species and impact in the pathogenesis of endometriosis. This study investigated the association of mtDNA polymorphisms with endometriosis.

METHODS

Patients were divided in two groups: endometriosis (n = 90) and control (n = 92). Inclusion criteria were as follows: women between 18 and 50 years, with histological diagnosis and surgical staging of endometriosis (endometriosis group) or undergoing gynecological surgery for tubal ligation, leiomyoma, or ovarian cysts, with no evidence of endometriosis (control group). DNA extraction was performed from peripheral blood. Sanger sequencing of mtDNA control region was performed, and polymorphisms were determined comparing the sequences obtained with the Cambridge Reference Sequence.

RESULTS

The frequency of polymorphisms T16217C (14.4 and 5.4% of endometriosis and control group, respectively; p = 0.049) and G499A (13.3 vs. 4.3%; p = 0.038) was higher in the endometriosis group, while T146C (32.6 vs. 18.9%; p = 0.042) and 573.2C (5.6 vs. 29.3%; p < 0.001) were lower. No difference was observed in haplogroups between groups.

CONCLUSION

mtDNA polymorphisms T16217C and G499A were associated with endometriosis, while T416C and 573.2C were shown to be associated with an absence of disease.

High Y-chromosomal Differentiation Among Ethnic Groups of Dir and Swat Districts, Pakistan

The ethnic groups that inhabit the mountainous Dir and Swat districts of northern Pakistan are marked by high levels of cultural and phenotypic diversity. To obtain knowledge of the extent of genetic diversity in this region, we investigated Y-chromosomal diversity in five population samples representing the three main ethnic groups residing within these districts, including Gujars, Pashtuns and Kohistanis. A total of 27 Y-chromosomal short tandem repeats (Y-STRs) and 331 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) were investigated. In the Y-STRs, we observed very high and significant levels of genetic differentiation in nine of the 10 pairwise between-group comparisons (R_ST 0.179-0.746), and the differences were mirrored in the Y-SNP haplogroup frequency distribution. No genetic differences were found between the two Pashtun subethnic groups Tarklanis and Yusafzais (R_ST = 0.000). Utmankhels, also considered Pashtuns culturally, were not closely related to any of the other population samples (R_ST 0.451-0.746). Thus, our findings provide examples of both associations and dissociations between cultural and genetic legacies. When analyzed within a larger continental-scale context, these five ethnic groups fall mostly outside the previously characterized Y-chromosomal gene pools of the Indo-Pakistani subcontinent. Male founder effects, coupled with culturally and topographically based constraints upon marriage and movement, are likely responsible for the high degree of genetic structure in this region.

Hepatitis C virus pharmacogenomics in Latin American populations: implications in the era of direct-acting antivirals

In recent years, great progress has been made in the field of new therapeutic options for hepatitis C virus (HCV) infection. The new direct-acting antiviral agents (DAAs) represent a great hope for millions of chronically infected individuals because their use may lead to excellent cure rates with fewer side effects. In Latin America, the high prevalence of HCV genotype 1 infection and the significant association of Native American ancestry with risk predictive single-nucleotide polymorphisms (SNPs) in IFNL4 and ITPA genes highlight the need to implement new treatment regimens in these populations. However, the universal accessibility to DAAs is still not a reality in the region as their high cost is one of the major, although not the only, limiting factors for their broad implementation. Therefore, under these circumstances, could the assessment of host genetic markers be a useful tool to prioritize DAA treatment until global access to these new drugs can be achieved? This review will summarize the scientific evidences and the potential implications of HCV pharmacogenomics in this rapidly evolving era of anti-HCV drug development.

A South American Prehistoric Mitogenome: Context, Continuity, and the Origin of Haplogroup C1d

Based on mitochondrial DNA (mtDNA), it has been estimated that at least 15 founder haplogroups peopled the Americas. Subhaplogroup C1d3 was defined based on the mitogenome of a living individual from Uruguay that carried a lineage previously identified in hypervariable region I sequences from ancient and modern Uruguayan individuals. When complete mitogenomes were studied, additional substitutions were found in the coding region of the mitochondrial genome. Using a complete ancient mitogenome and three modern mitogenomes, we aim to clarify the ancestral state of subhaplogroup C1d3 and to better understand the peopling of the region of the Río de la Plata basin, as well as of the builders of the mounds from which the ancient individuals were recovered. The ancient mitogenome, belonging to a female dated to 1,610±46 years before present, was identical to the mitogenome of one of the modern individuals. All individuals share the mutations defining subhaplogroup C1d3. We estimated an age of 8,974 (5,748–12,261) years for the most recent common ancestor of C1d3, in agreement with the initial peopling of the geographic region. No individuals belonging to the defined lineage were found outside of Uruguay, which raises questions regarding the mobility of the prehistoric inhabitants of the country. Moreover, the present study shows the continuity of Native lineages over at least 6,000 years.