Dysplastic melanocytic nevus: Are molecular findings the key to the diagnosis?

The primary differential diagnosis of melanoma is dysplastic nevus. Until now, the final diagnosis is based on histological findings. With modern techniques, pathologists receive very early melanocytic lesions, which do not fit all malignant criteria. In those cases, even the concurrence between specialists and intraobserver agreement is not good. A molecular test could be developed to improve the accuracy of melanocytic lesions diagnosis and help in challenging lesions. The objective of this study is to provide a literary review looking for molecular markers that characterize dysplastic nevi and could help surgical pathologists differentiate them from melanoma. Articles from PubMed presenting case series of dysplastic nevi and melanoma genomic analyses were considered. The search was conducted in PubMed looking for papers written in English, published in the ten years preceding April 2020. This review confirmed the absence of a pathognomonic molecular marker of dysplastic nevi. This is a heterogeneous group of lesions with an uncertain risk to become a melanoma. The molecular heterogeneity of dysplastic nevi, the variation of histological diagnostic criteria among services, and the diverse molecular techniques applied are challenging features that might hamper definitive diagnoses. However, currently, there appears to be limited value for molecular testing in the diagnosis of dysplastic nevi.

Genetic variation (population database) at 20 autosomal STR loci in the population of Rajasthan (north-western India).

To explore the genetic diversity and establish the allelic database of the population of Rajasthan, we assessed 571 randomly selected unrelated healthy individuals residing in the state. Blood samples of the selected individuals were collected with the compliance of ethical standards. Locus Penta E was observed to be the most polymorphic (0.908), whereas locus TPOX was observed to be the least polymorphic (0.639). The observed heterozygosity ranged from a minimum of 0.667 (TPOX) to a maximum of 0.925 (Penta E). The combined value of the power of discrimination (PD) and power of exclusion (PE) for all the studied 20 short tandem repeat (STR) loci were observed to be 1 and 0.999999997560235 respectively. The combined values of matching probability (PM) and paternity index (PI) for all the studied 20 STR loci were 7 × 10-26 and 4 × 108 respectively. The obtained genetic data are useful for forensic DNA applications and expected to enrich the genetic database of Indian populations.

The insulin-like growth factor 2 gene and locus in nonmammalian vertebrates: Organizational simplicity with duplication but limited divergence in fish.

The small, secreted peptide, insulin-like growth factor 2 (IGF2), is essential for fetal and prenatal growth in humans and other mammals. Human IGF2 and mouse Igf2 genes are located within a conserved linkage group and are regulated by parental imprinting, with IGF2/Igf2 being expressed from the paternally derived chromosome, and H19 from the maternal chromosome. Here, data retrieved from genomic and gene expression repositories were used to examine the Igf2 gene and locus in 8 terrestrial vertebrates, 11 ray-finned fish, and 1 lobe-finned fish representing >500 million years of evolutionary diversification. The analysis revealed that vertebrate Igf2 genes are simpler than their mammalian counterparts, having fewer exons and lacking multiple gene promoters. Igf2 genes are conserved among these species, especially in protein-coding regions, and IGF2 proteins also are conserved, although less so in fish than in terrestrial vertebrates. The Igf2 locus in terrestrial vertebrates shares additional genes with its mammalian counterparts, including tyrosine hydroxylase (Th), insulin (Ins), mitochondrial ribosomal protein L23 (Mrpl23), and troponin T3, fast skeletal type (Tnnt3), and both Th and Mrpl23 are present in the Igf2 locus in fish. Taken together, these observations support the idea that a recognizable Igf2 was present in the earliest vertebrate ancestors, but that other features developed and diversified in the gene and locus with speciation, especially in mammals. This study also highlights the need for correcting inaccuracies in genome databases to maximize our ability to accurately assess contributions of individual genes and multigene families toward evolution, physiology, and disease.

The complex genetics of human insulin-like growth factor 2 are not reflected in public databases.

Recent advances in genetics present unique opportunities for enhancing knowledge about human physiology and disease susceptibility. Understanding this information at the individual gene level is challenging and requires extracting, collating, and interpreting data from a variety of public gene repositories. Here, I illustrate this challenge by analyzing the gene for human insulin-like growth factor 2 (IGF2) through the lens of several databases. IGF2, a 67-amino acid secreted peptide, is essential for normal prenatal growth and is involved in other physiological and pathophysiological processes in humans. Surprisingly, none of the genetic databases accurately described or completely delineated human IGF2 gene structure or transcript expression, even though all relevant information could be found in the published literature. Although IGF2 shares multiple features with the mouse Igf2 gene, it has several unique properties, including transcription from five promoters. Both genes undergo parental imprinting, with IGF2/Igf2 being expressed primarily from the paternal chromosome and the adjacent H19 gene from the maternal chromosome. Unlike mouse Igf2, whose expression declines after birth, human IGF2 remains active throughout life. This characteristic has been attributed to a unique human gene promoter that escapes imprinting, but as shown here, it involves several different promoters with distinct tissue-specific expression patterns. Because new testable hypotheses could lead to critical insights into IGF2 actions in human physiology and disease, it is incumbent that our fundamental understanding is accurate. Similar challenges affecting knowledge of other human genes should promote attempts to critically evaluate, interpret, and correct human genetic data in publicly available databases.

Genome Database of the Latvian Population (LGDB): Design, Goals, and Primary Results.

BACKGROUND: The Genome Database of the Latvian Population (LGDB) is a national biobank that collects, maintains, and processes health information, data, and biospecimens collected from representatives of the Latvian population. These specimens serve as a foundation for epidemiological research and prophylactic and therapeutic purposes. METHODS: Participant recruitment and biomaterial and data processing were performed according to specifically designed standard protocols, taking into consideration international quality requirements. Legal and ethical aspects, including broad informed consent and personal data protection, were applied according to legal norms of the Republic of Latvia. RESULTS: Since its start in 2006, the LGDB is comprised of biosamples and associated phenotypic and clinical information from over 31,504 participants, constituting approximately 1.5% of the Latvian population. The LGDB represents a mixed-design biobank and includes participants from the general population as well as disease-based cohorts. The standard set of biosamples stored in the LGDB consists of DNA, plasma, serum, and white blood cells; in some cohorts, these samples are complemented by cancer biopsies and microbiome and urine samples. The LGDB acts as a core structure for the Latvian Biomedical Research and Study Centre (BMC), representing the national node of Latvia in Biobanking and BioMolecular resources Research Infrastructure - European Research Infrastructure Consortium (BBMRI-ERIC). CONCLUSIONS: The development of the LGDB has enabled resources for biomedical research and promoted genetic testing in Latvia. Further challenges of the LGDB are the enrichment and harmonization of collected biosamples and data, the follow-up of selected participant groups, and continued networking and participation in collaboration projects.

Genetic studies on the Cayo Santiago rhesus macaques: A review of 40 years of research.

Genetic studies not only contribute substantially to our current understanding of the natural variation in behavior and health in many species, they also provide the basis of numerous in vivo models of human traits. Despite the many challenges posed by the high level of biological and social complexity, a long lifespan and difficult access in the field, genetic studies of primates are particularly rewarding because of the close evolutionary relatedness of these species to humans. The free-ranging rhesus macaque (Macaca mulatta) population on Cayo Santiago (CS), Puerto Rico, provides a unique resource in this respect because several of the abovementioned caveats are of either minor importance there, or lacking altogether, thereby allowing long-term genetic research in a primate population under constant surveillance since 1956. This review summarizes more than 40 years of genetic research carried out on CS, from early blood group typing and the genetic characterization of skeletal material via population-wide paternity testing with DNA fingerprints and short tandem repeats (STRs) to the analysis of the highly polymorphic DQB1 locus within the major histocompatibility complex (MHC). The results of the paternity studies also facilitated subsequent studies of male dominance and other factors influencing male reproductive success, of male reproductive skew, paternal kin bias, and mechanisms of paternal kin recognition. More recently, the CS macaques have been the subjects of functional genetic and gene expression analyses and have played an important role in behavioral and quantitative genetic studies. In addition, the CS colony has been used as a natural model for human adult-onset macular degeneration, glaucoma, and circadian rhythm disorder. Our review finishes off with a discussion of potential future directions of research on CS, including the transition from STRs to single nucleotide polymorphism (SNP) typing and whole genome sequencing.

Prevalence estimation of ATTRv in China based on genetic databases.

Introduction: Amyloid transthyretin (ATTR) is divided into either hereditary (ATTRv) or sporadic (ATTRwt) and ATTRv is a rare hereditary disease transmitted as an autosomal dominant manner. Its global prevalence is traditionally estimated as 5,000 to 10,000 persons. However, it may be underestimated and the exact prevalence of ATTRv in China mainland remains unknown. Methods: The Genome Aggregation database (gnomAD) database (containing 125,748 exomes) and two genomic sequencing databases--China Metabolic Analytics Project (ChinaMAP) (containing 10588 individuals) and Amcarelab gene database (containing 45392 exomes), were integrated to estimate the prevalence of ATTRv in the world and mainland Chinese populations. Pathogenic variants allele frequency and the prevalence of ATTRv was calculated. Results: Six variants, counting 470 alleles, were defined as pathogenic variants in gnomAD. The prevalence of ATTRv in the world population was 57.4/100,000. Two variants (2 allele counts) and 15 variants (34 individuals) were defined as pathogenic variants in the ChinaMAP database and the Amcarelab exome database, respectively. Thus, the estimated prevalence interval of ATTRv in mainland China was 18.9/100,000-74,9/100,000. Conclusion: The present study demonstrated that the previous prevalence was greatly underestimated using traditional methods. Therefore, raising awareness of the disease is essential for recognizing ATTRv in its early stage.

The challenge of predicting human pigmentation traits in degraded bone samples with the MPS-based HIrisPlex-S system.

Identification of human remains is an important part of human DNA analysis studies. STR and mitochondrial DNA markers are well suited for the analysis of degraded biological samples including bone material. However, these DNA markers may be useless when reference material is not available. In these cases, predictive DNA analysis can support the process of human identification by providing investigative leads. Forensic DNA phenotyping has progressed significantly by offering new methods based on massively parallel sequencing technology, but the frequent degradation processes observed in skeletal remains can make analysis of such samples challenging. In this study, we demonstrate the usefulness of a recently established Ion AmpliSeqTM HIrisPlex-S panel using Ion Torrent technology for analyzing bone samples that show different levels of DNA degradation. In total, 63 bone samples at post-mortem intervals up to almost 80 years were genotyped and eye, hair and skin colour predictions were performed using the HIrisPlex-S models. Following the recommended coverage thresholds, it was possible to establish full DNA profiles comprising of 41 DNA variants for 35 samples (55.6%). For 5 samples (7.9%) no DNA profiles were generated. The remaining 23 samples (36.5%) produced partial profiles and showed a clear underperformance of 3 HIrisPlex-S SNPs - rs1545397 (OCA2), rs1470608 (OCA2) and rs10756819 (BNC2), all used for skin colour prediction only. None of the 23 samples gave complete genotypes needed for skin colour prediction was obtained, and in 7 of them (25.9%) the 3 underperformed SNPs were the cause. At the same time, the prediction of eye and hair colour using complete IrisPlex and HIrisPlex profiles could be made for these 23 samples in 20 (87.0%) and 12 cases (52.2%), respectively. Complete HIrisPlex-S profiles were generated from as little as 49 pg of template DNA. Five samples for which the HIrisPlex-S analysis failed, consistently failed in standard STR analysis. Importantly, the 3 underperforming SNPs produced significantly lower number of reads in good quality samples. Nonetheless, the AUC loss resulting from missing data for these 3 SNPs is not considered large (≤0.004) and the prediction of pigmentation from partial profiles is also available in the current HPS tool. The study shows that DNA degradation and the resulting loss of data are the most serious challenge to DNA phenotyping of skeletal remains. Although the newly developed HIrisPlex-S panel has been successfully validated in the current research, primer redesign for the 3 underperforming SNPs in the MPS design should be considered in the future.

The Polish Genetic Database of Victims of Totalitarianisms.

This paper describes the creation of the Polish Genetic Database of Victims of Totalitarianism and the first research conducted under this project. On September 28th 2012, the Pomeranian Medical University in Szczecin and the Institute of National Remembrance-Commission for Prosecution of Crimes against the Polish Nation agreed to support the creation of the Polish Genetic Database of Victims of Totalitarianism (PBGOT, www.pbgot.pl). The purpose was to employ state-of-the-art methods of forensic genetics to identify the remains of unidentified victims of Communist and Nazi totalitarian regimes. The database was designed to serve as a central repository of genetic information of the victim's DNA and that of the victim's nearest living relatives, with the goal of making a positive identification of the victim. Along the way, PGBOT encountered several challenges. First, extracting useable DNA samples from the remains of individuals who had been buried for over half a century required forensic geneticists to create special procedures and protocols. Second, obtaining genetic reference material and historical information from the victim's closest relatives was both problematic and urgent. The victim's nearest living relatives were part of a dying generation, and the opportunity to obtain the best genetic and historical information about the victims would soon die with them. For this undertaking, PGBOT assembled a team of historians, archaeologists, forensic anthropologists, and forensic geneticists from several European research institutions. The field work was divided into five broad categories: (1) exhumation of victim remains and storing their biological material for later genetic testing; (2) researching archives and historical data for a more complete profile of those killed or missing and the families that lost them; (3) locating the victim's nearest relatives to obtain genetic reference samples (swabs), (4) entering the genetic data from both victims and family members into a common database; (5) making a conclusive, final identification of the victim. PGBOT's first project was to identify victims of the Communist regime buried in hidden mass graves in the Powazki Military Cemetery in Warsaw. Throughout 2012 and 2013, PGBOT carried out archaeological exhumations in the Powazki Military Cemetery that resulted in the recovery of the skeletal remains of 194 victims in several mass graves. Of the 194 sets of remains, more than 50 victims have been successfully matched and identified through genetic evidence.

NABIC marker database: A molecular markers information network of agricultural crops.

UNLABELLED: In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. AVAILABILITY: The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

BDgene: a genetic database for bipolar disorder and its overlap with schizophrenia and major depressive disorder.

BACKGROUND: Bipolar disorder (BD) is a common psychiatric disorder with complex genetic architecture. It shares overlapping genetic influences with schizophrenia (SZ) and major depressive disorder (MDD). Large numbers of genetic studies of BD and cross-disorder studies between BD and SZ/MDD have accumulated numerous genetic data. There is a growing need to integrate the data to provide a comprehensive data set to facilitate the genetic study of BD and its highly relevant diseases. METHODS: BDgene database was developed to integrate BD-related genetic factors and shared ones with SZ/MDD from profound literature reading. On the basis of data from the literature, in-depth analyses were performed for further understanding of the data, including gene prioritization, pathway-based analysis, intersection analysis of multidisease candidate genes, and pathway enrichment analysis. RESULTS: BDgene includes multiple types of literature-reported genetic factors of BD with both positive and negative results, including 797 genes, 3119 single nucleotide polymorphisms, and 789 regions. Shared genetic factors such as single nucleotide polymorphisms, genes, and regions from published cross-disorder studies among BD and SZ/MDD were also presented. In-depth data analyses identified 43 BD core genes; 70 BD candidate pathways; and 127, 79, and 107 new potential cross-disorder genes for BD-SZ, BD-MDD, and BD-SZ-MDD, respectively. CONCLUSIONS: As a central genetic database for BD and the first cross-disorder database for BD and SZ/MDD, BDgene provides not only a comprehensive review of current genetic research but also high-confidence candidate genes and pathways for understanding of BD mechanism and shared etiology among its relevant diseases. BDgene is freely available at http://bdgene.psych.ac.cn.

Investigação das características moleculares e filogenéticas dos isolamentos de Pythium insidiosum em casos de ceratite / Investigation of the molecular and phylogenetic characteristics of Pythium insidiosum isolates in cases of keratitis

Introdução: Pythium insidiosum é um microrganismo fenotipicamente semelhante aos fungos com hifas, mas este oomyceto pertencente ao filo Straminofila, filogeneticamente separado dos fungos verdadeiros. Usando metodologias moleculares, isolados de P. insidiosum foram colocados em três grupos filogenéticos de acordo com sua distribuição geográfica. Mais recentemente, quatro grupos filogenéticos foram relatados. Pythium insidiosum é capaz de causar infecções graves em humanos. Pode acometer os olhos na forma de ceratites e infecções dos tecidos adjacentes que ameaçam não apenas a visão, mas também a vida do paciente. Devido ao desenvolvimento de hifas, frequentemente a infecção por esse patógeno é confundida e diagnosticada erroneamente como infecção fúngica. Objetivo: Investigar as características moleculares e filogenéticas dos isolamentos de P. insidiosum recuperados de quatorze amostras coletadas na Índia em casos de ceratite. Materiais e Métodos: Foram avaliados quatorze isolamentos de P. insidiosum dos quais foram extraídos o DNA e, então, realizados PCR com primers universais. Prosseguiu-se com amplificação das sequências utilizando Internal Transcriber Spacers (ITS) e Citocromo C Oxidase subunidade II (COXII). As análises filogenéticas subsequentes, utilizando as sequências de ITS e COXII, foram analisadas pelo método estatístico Neighbor Joining (MEGAX). Resultados: As árvores filogenéticas usando as sequências de DNA amplificadas (ITS e COXII) mostraram resultados análogos. As sequências provenientes dos quatorze isolamentos analisados foram especificamente colocadas, com alto suporte de bootstrap, no grupo II (Ásia, Austrália e África) e no grupo IV (Tailândia, Israel), de acordo com a divisão atual de P. insidiosum. Do total dos quatorze isolamentos, dez foram colocados no grupo II e quatro no grupo IV. Interessantemente, nenhum dos isolamentos foi colocado nos grupos I e III (Américas). Foi possível comprovar que os dez isolados neste estudo foram identificados como P. insidiosum comprovando a hipótese inicial. No entanto, como foi postulado anteriormente, ao avaliar as quatro sequências localizadas no grupo IV a existência de uma espécie inteiramente nova é fortemente suportada. Para confirmar essa hipótese, são necessários novos estudos baseados em análises estatísticas. Conclusão: Pacientes com ceratite resistente ao tratamento convencional, de rápida evolução, com cultura de padrão de crescimento com presença de micélios submersos aderidos ao ágar devem alertar sobre a possibilidade de infecção por P. insidiosum. Para a confirmação de possíveis isolados de P. insidiosum, técnicas moleculares devem ser realizadas. Esses foram os passos seguidos no presente estudo tornando possível a identificação do agente etiológico das ceratites da Índia como P. insidiosum. Além disso, as técnicas filogenéticas usadas neste e em outros estudos, sugeriram a possibilidade de uma nova espécie dentro do complexo P. insidiosum, o que provavelmente é uma das contribuições mais importantes deste estudo.

Introduction: Pythium insidiosum is a microorganism phenotypically like fungi with hyphae, but this oomycete belongs to the phylum Straminopila phylogenetically away from true fungi. Using molecular methodologies, isolates of P. insidiosum were placed in three phylogenetic groups according to their geographic distribution. More recently, four phylogenetic groups were reported. Pythium insidiosum can cause serious infections in humans. It can affect the eyes in the form of keratitis and infections of adjacent tissues that threaten not only the eyesight, but also the patient's life. Due to the development of hyphae, infection with this pathogen is often mistaken and misdiagnosed as a fungal infection. Objective: To investigate the molecular and phylogenetic characteristics of the isolates of P. insidiosum recovered from fourteen samples collected in Indian cases of keratitis. Materials and Methods: Fourteen P. insidiosum isolates were evaluated, from which DNA was extracted and then PCR with universal primers was performed. PCR amplification was performed using Internal Transcriber Spacers (ITS) and Cytochrome C Oxidase S subunit II (COXII) primers and subsequently sequenced. Phylogenetic analyzes, using the aligned ITS and COXII sequences, were analyzed by the Neighbor Joining method (MEGAX). Results: Phylogenetic trees using the amplified DNA sequences (ITS and COXII) showed similar results. The DNA sequences from the fourteen analyzed isolates were specifically placed, with high bootstrap support, in group II (Asia, Australia and Africa) and in group IV (Thailand, Israel), according to the current phylogenetic cluster classification of P. insidiosum. Of the fourteen isolates, ten were placed in cluster II, and four of them in cluster IV. Interestingly, none of the isolations were placed in clusters I and III (The Americas). The ten isolates in this study were identified as P. insidiosum, which support the initial hypothesis. As was previously postulated, this study found that the four Indian DNA sequences located in cluster IV represent an entirely new specie. To confirm this finding, further studies based on statistical analysis are needed. Conclusion: Patients with keratitis of rapid clinical progression, resistant to conventional treatment, with the presence of submerged mycelia adhered to the agar should alert clinicians about the possibility of infection caused by P. insidiosum. To identify possible P. insidiosum isolates, molecular techniques must be performed. Molecular and phylogenetic analyses were used in the present study making it possible to identify the etiological agent of keratitis in India as P. insidiosum. In addition, phylogenetic analyses in this and other studies, suggested the possibility of a new species within P. insidiosum complex, which is probably one of the most important contributions of this study.