Analysis Of Genetic Markers Research Articles

Novel Methods for Family-Based Genetic Studies.

The recent development of microarray and sequencing technology allows identification of disease susceptibility genes. Although the genome-wide association studies (GWAS) have successfully identified many genetic markers related to human diseases, the traditional statistical methods are not powerful to detect rare genetic markers. The rare genetic markers are usually grouped together and tested at the set level. One of such methods is the sequence kernel association test (SKAT), which has been commonly used in the rare genetic marker analysis. In recent publications, SKAT has been extended to be applicable for family-based rare variant analysis. Here, I present three published statistical approaches for family-based rare variant analysis for: 1. continuous traits, 2. binary traits, and 3. multiple correlated traits.

Real-Time and Non-invasive Monitoring of the Activation of the IRE1α-XBP1 Pathway in Individuals with Hemodynamic Impairment

Many stressors that are encountered upon kidney injury are likely to trigger endoplasmic reticulum (ER) stress, subsequently activating transcriptional, translational and metabolic reprogramming. Monitoring early cellular adaptive responses engaged after hemodynamic impairment yields may represent a clinically relevant approach. However, a non-invasive method for detecting the ER stress response has not been developed. We combined a metabolomic approach with genetic marker analyses using urine from individuals undergoing scheduled cardiac surgery under cardiopulmonary bypass to investigate the feasibility and significance of monitoring the ER stress response in the kidney. We developed an original method based on fragment analysis that measures urinary levels of the spliced X-box binding protein 1 (sXBP1) mRNA as a proxy of inositol-requiring enzyme 1α (IRE1α) activity because sXBP1 is absolutely sensitive and specific for ER stress. The early engagement of the ER stress response after ischemic stress is critical for protecting against tissue damage, and individuals who mount a robust adaptive response are protected against AKI. The clinical consequences of our findings are of considerable importance because ER stress is involved in numerous conditions that lead to AKI and chronic kidney disease; in addition, the detection of ER stress is straightforward and immediately available in routine practice.

Thorough analysis of unorthodox ABO deletions called by the 1000 Genomes project.

ABO remains the clinically most important blood group system, but despite earlier extensive research, significant findings are still being made. The vast majority of catalogued ABO null alleles are based on the c.261delG polymorphism. Apart from c.802G>A, other mechanisms for O alleles are rare. While analysing the data set from the 1000 Genomes (1000G) project, we encountered two previously uncharacterized deletions, which needed further exploration. The Erythrogene database, complemented with bioinformatics software, was used to analyse ABO in 2504 individuals from 1000G. DNA samples from selected 1000G donors and African blood donors were examined by allele-specific PCR and Sanger sequencing to characterize predicted deletions. A 5821-bp deletion encompassing exons 5-7 was called in twenty 1000G individuals, predominantly Africans. This allele was confirmed and its exact deletion point defined by bioinformatic analyses and invitro experiments. A PCR assay was developed, and screening of African samples revealed three donors heterozygous for this deletion, which was thereby phenotypically established as an O allele. Analysis of upstream genetic markers indicated an ancestral origin from ABO*O.01.02. We estimate this deletion as the 3rd most common mechanism behind O alleles. A 24-bp deletion was called in nine individuals and showed greater diversity regarding ethnic distribution and allelic background. It could neither be confirmed by in silico nor invitro experiments. A previously uncharacterized ABO deletion among Africans was comprehensively mapped and a genotyping strategy devised. The false prediction of another deletion emphasizes the need for cautious interpretation of NGS data and calls for strict validation routines.

Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans

The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5th century BCE [1-3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6-8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7th-11th centuries CE)yielded sufficient autosomal genome coverage (0.21× to 3.93×) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%-31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.

Genetic identification of a newly synthetic allopolyploid strain with 206 chromosomes in polyploid gibel carp

A newly synthetic allopolyploid strain (SAS) was selected and established from gynogenetic offspring of gibel carp clone A+ with 156 chromosomes induced by common carp sperm with 50 chromosomes. In this study, the allopolyploid strain was detected to contain 206 chromosomes, and the growth trait was evaluated to have 25.15% growth faster than that of clone A+. Genetic marker analyses of transferrin (Tf) alleles, ITS1 sequences and mtDNA D-loop sequences indicated that the allopolyploid strain was synthetized from maternal gibel carp clone A+ and paternal common carp, and the synthetic chromosome sets were further confirmed by genomic in situ hybridization (GISH) and chromosome localization of 45S rDNA. Significantly, the synthetic allopolyploid strain has tended to be stable by five successive generations of gynogenesis, because it still keeps unisexual reproduction mode of gynogenesis. Therefore, it will become a novel variety for gibel carp aquaculture in future.

Girardia dorotocephala transcriptome sequence, assembly, and validation through characterization of piwi homologs and stem cell progeny markers

Planarian flatworms are popular models for the study of regeneration and stem cell biology in vivo. Technical advances and increased availability of genetic information have fueled the discovery of molecules responsible for stem cell pluripotency and regeneration in flatworms. Unfortunately, most of the planarian research performed worldwide utilizes species that are not natural habitants of North America, which limits their availability to newcomer laboratories and impedes their distribution for educational activities. In order to circumvent these limitations and increase the genetic information available for comparative studies, we sequenced the transcriptome of Girardia dorotocephala, a planarian species pandemic and commercially available in North America. A total of 254,802,670 paired sequence reads were obtained from RNA extracted from intact individuals, regenerating fragments, as well as freshly excised auricles of a clonal line of G. dorotocephala (MA-C2), and used for de novo assembly of its transcriptome. The resulting transcriptome draft was validated through functional analysis of genetic markers of stem cells and their progeny in G. dorotocephala. Akin to orthologs in other planarian species, G. dorotocephala Piwi1 (GdPiwi1) was found to be a robust marker of the planarian stem cell population and GdPiwi2 an essential component for stem cell-driven regeneration. Identification of G. dorotocephala homologs of the early stem cell descendent marker PROG-1 revealed a family of lysine-rich proteins expressed during epithelial cell differentiation. Sequences from the MA-C2 transcriptome were found to be 98–99% identical to nucleotide sequences from G. dorotocephala populations with different chromosomal number, demonstrating strong conservation regardless of karyotype evolution. Altogether, this work establishes G. dorotocephala as a viable and accessible option for analysis of gene function in North America.

Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes

BackgroundForage species of Urochloa are planted in millions of hectares of tropical and subtropical pastures in South America. Most of the planted area is covered with four species (U. ruziziensis, U. brizantha, U. decumbens and U. humidicola). Breeding programs rely on interspecific hybridizations to increase genetic diversity and introgress traits of agronomic importance. Knowledge of phylogenetic relationships is important to optimize compatible hybridizations in Urochloa, where phylogeny has been subject of some controversy. We used next-generation sequencing to assemble the chloroplast genomes of four Urochloa species to investigate their phylogenetic relationships, compute their times of divergence and identify chloroplast DNA markers (microsatellites, SNPs and InDels).ResultsWhole plastid genome sizes were 138,765 bp in U. ruziziensis, 138,945 bp in U. decumbens, 138,946 bp in U. brizantha and 138,976 bp in U. humidicola. Each Urochloa chloroplast genome contained 130 predicted coding regions and structural features that are typical of Panicoid grasses. U. brizantha and U. decumbens chloroplast sequences are highly similar and show reduced SNP, InDel and SSR polymorphism as compared to U. ruziziensis and U. humidicola. Most of the structural and sequence polymorphisms were located in intergenic regions, and reflected phylogenetic distances between species. Divergence of U. humidicola from a common ancestor with the three other Urochloa species was estimated at 9.46 mya. U. ruziziensis, U. decumbens, and U. brizantha formed a clade where the U. ruziziensis lineage would have diverged by 5.67 mya, followed by a recent divergence event between U. decumbens and U. brizantha around 1.6 mya.ConclusionLow-coverage Illumina sequencing allowed the successful sequence analysis of plastid genomes in four species of Urochloa used as forages in the tropics. Pairwise sequence comparisons detected multiple microsatellite, SNP and InDel sites prone to be used as molecular markers in genetic analysis of Urochloa. Our results placed the origin of U. humidicola and U. ruziziensis divergence in the Miocene-Pliocene boundary, and the split between U. brizantha and U. decumbens in the Pleistocene.

Sensitivity and accuracy of high-throughput metabarcoding methods for early detection of invasive fish species

High-throughput DNA metabarcoding has gained recognition as a potentially powerful tool for biomonitoring, including early detection of aquatic invasive species (AIS). DNA based techniques are advancing, but our understanding of the limits to detection for metabarcoding complex samples is inadequate. For detecting AIS at an early stage of invasion when the species is rare, accuracy at low detection limits is key. To evaluate the utility of metabarcoding in future fish community monitoring programs, we conducted several experiments to determine the sensitivity and accuracy of routine metabarcoding methods. Experimental mixes used larval fish tissue from multiple “common” species spiked with varying proportions of tissue from an additional “rare” species. Pyrosequencing of genetic marker, COI (cytochrome c oxidase subunit I) and subsequent sequence data analysis provided experimental evidence of low-level detection of the target “rare” species at biomass percentages as low as 0.02% of total sample biomass. Limits to detection varied interspecifically and were susceptible to amplification bias. Moreover, results showed some data processing methods can skew sequence-based biodiversity measurements from corresponding relative biomass abundances and increase false absences. We suggest caution in interpreting presence/absence and relative abundance in larval fish assemblages until metabarcoding methods are optimized for accuracy and precision.

To what extent do wild apples in Kazakhstan retain their genetic integrity?

Kazakhstan belongs to the center of origin of apple. Malus sieversii (Ledeb.) M. Roem., the ancestral progenitor of the cultivated apple is native to this region. Pressure on the natural habitats of this wild apple has been intensified due to agriculture, grazing, and urbanization in the last century. For decades, M. sieversii in Kazakhstan has been subjected to the “Red Book of the Kazakh SSR” and today, this species is threatened with extinction. Wild apple undergoes exceptional losses in habitats, and the risk for losing the genetic integrity becomes worse due to increasing cultivation of cultivated apples and frequently occurring crosspollination events. The present study was focused on the current state of M. sieversii in Kazakhstan, the level of its diversity, its genetic integrity, and the identification of regions where future activities for conservation will have a good chance of success. A total of 311 M. sieversii samples of 12 populations collected in the wild, 16 previously selected wild apple genotypes, and 50 grown cultivars were studied using 16 simple sequence repeat (SSR) markers for genetic analysis. The results suggest that the level of genetic diversity is high. The differentiation between the populations was low, although the within-population heterozygosity was relatively high. A significant number of hybrids (8–95%) between M. sieversii and cultivated apples were found suggesting frequent crop-to-wild gene flow. The percentage of pure wild apple genotypes was highest in Krutoe truct and Tauturgen. These sites should be taken into account for future in situ long-term preservation activities.

Genetic predictors of cardiovascular system adaptation in adolescents to physical stress

Aim. Analysis of genetic markers of physical performance and their interrelation with electrocardiographic parameters in athletes of the youth league.Methods. The study involved 204 of adolescent athletes. EKGs were performed, the profile of genes of folate cycle and genes encoding the function of angiotensin-converting enzyme was detected by polymerase chain reaction in venous blood.Results. It was found that all participants had sinus rhythm. Arrhythmias and conduction disorders were revealed: bradycardia was observed in 22 (10.7%) of participants, normocardia - in 168 (82%) participants, tachycardia - in 14 (6.8%) participants, incomplete right and left bundle branch block - in 16 (7.7%) participants, and repolarization disorders of left ventricle - in 5 (2.4%) young athletes. The genes polymorphism of folate cycle and genes encoding the function of angiotensin-converting enzyme in the examined individuals were presented in different variants. Majority of the participants had heterozygous forms in most genes except for the gene NOS3 894 GT presented as a dominant form.Conclusion. Accordng to EKG the athletes of the youth league had early repolarization of the left ventricle (2.4% cases), incomplete right or left bundle branch block (7.7% cases), and normal waves and intervals; according to genetic study most participants had heterozygous genotype GNB3 825 CT, NOS3-786 TC, AGT 704 TC, negative correlation of QTc with NOS3-786 TC and NOS3 894 GT, α-angle / AGT 704 TC with P-wave / NOS3 894 GT.

Morphological and molecular identification of Explanatum explanatum in domestic water buffalo in Pakistan.

More than 70 species of the family Paramphistomatidae, have been identified in ruminants in different parts of the world. Most are pathogenic, causing amphistomosis. Adult flukes of this Family have a predilection for the rumen, liver or bile duct of ruminants where they may cause damage to the epithelium. Identification of adult paramphistomes to the species level based on morphology alone requires specialized knowledge, whereas, molecular genetic marker analysis is more precise and transferable. In the present study, we performed both morphological and molecular characterization of fifteen adult flukes collected from the liver of domesticated buffalo in the Punjab province of Pakistan. The morphology of five of these flukes was examined in detail and on this basis these were identified as either Explanatum explanatum or Explanatum bathycotyle. PCR and sequencing of the ITS-2 rDNA region from these 5 flukes, plus 10 others, revealed a single haplotype in all cases. This differed by just a single nucleotide polymorphism from a previously described E. explanatum ITS-2 rDNA sequence. Phylogenetic comparison of these E. explanatum ITS2-rDNA sequences with those from other Paramphistomatidae, Fasciola and Dicrocoelium species was performed to assess within and between species variation and validate the use of ITS-2 rDNA as a robust species-specific marker for E. explanatum. This work provides a validated species-specific marker of E. explanatum and the first report of this parasite species from Pakistan.

Bayesian longitudinal low-rank regression models for imaging genetic data from longitudinal studies

To perform a joint analysis of multivariate neuroimaging phenotypes and candidate genetic markers obtained from longitudinal studies, we develop a Bayesian longitudinal low-rank regression (L2R2) model. The L2R2 model integrates three key methodologies: a low-rank matrix for approximating the high-dimensional regression coefficient matrices corresponding to the genetic main effects and their interactions with time, penalized splines for characterizing the overall time effect, and a sparse factor analysis model coupled with random effects for capturing within-subject spatio-temporal correlations of longitudinal phenotypes. Posterior computation proceeds via an efficient Markov chain Monte Carlo algorithm. Simulations show that the L2R2 model outperforms several other competing methods. We apply the L2R2 model to investigate the effect of single nucleotide polymorphisms (SNPs) on the top 10 and top 40 previously reported Alzheimer disease-associated genes. We also identify associations between the interactions of these SNPs with patient age and the tissue volumes of 93 regions of interest from patients’ brain images obtained from the Alzheimer's Disease Neuroimaging Initiative.

Establishment of apoptotic regulatory network for genetic markers of colorectal cancer.

Our purpose is to screen out genetic markers applicable to early diagnosis for colorectal cancer and to establish apoptotic regulatory network model for colorectal cancer, thereby providing theoretical evidence and targeted therapy for early diagnosis of colorectal cancer. Taking databases including CNKI, VIP, Wanfang data, Pub Med, and MEDLINE as main sources of literature retrieval, literatures associated with genetic markers applied to early diagnosis of colorectal cancer were searched to perform comprehensive and quantitative analysis by Meta analysis, hence screening genetic markers used in early diagnosis of colorectal cancer. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were employed to establish apoptotic regulatory network model based on screened genetic markers, and then verification experiment was conducted. Through Meta analysis, seven genetic markers were screened out, including WWOX, K-ras, COX-2, p53, APC, DCC and PTEN, among which DCC shows highest diagnostic efficiency. GO analysis of genetic markers found that six genetic markers played role in biological process, molecular function and cellular component. It was indicated in apoptotic regulatory network built by KEGG analysis and verification experiment that WWOX could promote tumor cell apoptotic in colorectal cancer and elevate expression level of p53. The apoptotic regulatory model of colorectal cancer established in this study provides clinically theoretical evidence and targeted therapy for early diagnosis of colorectal cancer.

Early Detection of Nonnative Alleles in Fish Populations: When Sample Size Actually Matters

Reliable detection of nonnative alleles is crucial for the conservation of sensitive native fish populations at risk of introgression. Typically, nonnative alleles in a population are detected through the analysis of genetic markers in a sample of individuals. Here we show that common assumptions associated with such analyses yield substantial overestimates of the likelihood of detecting nonnative alleles. We present a revised equation to estimate the likelihood of detecting nonnative alleles in a population with a given level of admixture. The new equation incorporates the effects of the genotypic structure of the sampled population and shows that conventional methods overestimate the likelihood of detection, especially when nonnative or F‐1 hybrid individuals are present. Under such circumstances—which are typical of early stages of introgression and therefore most important for conservation efforts—our results show that improved detection of nonnative alleles arises primarily from increasing the number of individuals sampled rather than increasing the number of genetic markers analyzed. Using the revised equation, we describe a new approach to determining the number of individuals to sample and the number of diagnostic markers to analyze when attempting to monitor the arrival of nonnative alleles in native populations.

Korean Brain Aging Study for the Early Diagnosis and Prediction of Alzheimer's Disease: Methodology and Baseline Sample Characteristics.

ObjectiveThe Korean Brain Aging Study for the Early Diagnosis and Prediction of Alzheimer's disease (KBASE) aimed to recruit 650 individuals, aged from 20 to 90 years, to search for new biomarkers of Alzheimer's disease (AD) and to investigate how multi-faceted lifetime experiences and bodily changes contribute to the brain changes or brain pathologies related to the AD process.MethodsAll participants received comprehensive clinical and neuropsychological evaluations, multi-modal brain imaging, including magnetic resonance imaging, magnetic resonance angiography, [11C]Pittsburgh compound B-positron emission tomography (PET), and [18F]fluorodeoxyglucose-PET, blood and genetic marker analyses at baseline, and a subset of participants underwent actigraph monitoring and completed a sleep diary. Participants are to be followed annually with clinical and neuropsychological assessments, and biannually with the full KBASE assessment, including neuroimaging and laboratory tests.ResultsAs of March 2017, in total, 758 individuals had volunteered for this study. Among them, in total, 591 participants–291 cognitively normal (CN) old-aged individuals, 74 CN young- and middle-aged individuals, 139 individuals with mild cognitive impairment (MCI), and 87 individuals with AD dementia (ADD)–were enrolled at baseline, after excluding 162 individuals. A subset of participants (n=275) underwent actigraph monitoring.ConclusionThe KBASE cohort is a prospective, longitudinal cohort study that recruited participants with a wide age range and a wide distribution of cognitive status (CN, MCI, and ADD) and it has several strengths in its design and methodologies. Details of the recruitment, study methodology, and baseline sample characteristics are described in this paper.

Application of next generation sequencing in forensic science [Yeni nesil dizilemenin adli bilimlerde kullanimi

Next Generation Sequencing (NGS) Technology has been emerged and started to use in genetic research since the 2000s. Until today, various methods which are faster, high throughput and low cost have been developed. NGS Technologies have been gradually developed and the quality of sequencing has been reached the high level and forensic genetics labs have moved to this technology for recent years. NGS Technologies provide new opportunities for forensic genetics research. NGS Technologies enable to analysis of many forensic genetic markers (as STRs, SNPs, mRNA) in only one experiment. Besides, NGS technologies are applicable for different practices which are essential in forensic researches. Among these, create of a DNA database, ancestry and phenotype studies, monozygotic twin studies, identification of body fluids and species, forensic microbiology studies can be considered. This review has been written to focus on NGS technologies in forensic genetics applications and to be a reference study for next forensic researchers.

M15 - Overlapping Pattern of Genetic Associations of Alzheimer’s Disease And Schizophrenia Mediated By Cognitive Endophenotypes Genes

Background Replicative analysis of genetic markers, previously identified in genome-wide association studies (GWAS) for neuropsychiatric diseases, in population of various origin may contribute to better understanding of genetic composition of the diseases. Methods In this study 50 SNPs found in GWAS for schizophrenia (SZ), Alzheimer’s diseases (AD) and cognitive endophenotypes were genotyped in patients and control samples from Russian and Kazakh populations. Genotyping was performed by TaqMan assays and MALDI-TOF mass-spectrometry. Results Eight polymorphic markers (SNPs in regions of genes for APOЕ, APOJ, CSMD1, CCDC60, SNX29, PICALM, NOTCH4 and NRIP1) were associated with AD in Russian population. Associations of 10 genetic markers with SZ in Russian populations (markers in regions of genes for NRGN, KCNB2, NRIP1, CCDC60, LSM1, LOC100129100 / LOC100509857, CSMD1, СPVL, POM121L2 and NDE1P1 / PRMT6) and 8 genetic markers in Kazakh population (VRK2, KCNB2, СPVL, BRD1, PVRL2, ARHGAP1, CD33 и GPR89P / TRV-AAC1-5) were replicated. Multidimensional reduction methods revealed epistatic interaction of several genetic loci in formation of susceptibility to SZ in populations of various ethnic origin. Discussion Overlapping fields of genetic associations for AD and SZ, demonstrating some similarity in inherited background for both diseases, were found. This interaction may be implemented through common unknown levels in pathogenesis of AD and SZ, mediated by cognitive endophenotypes. Bioinformatic analysis of biological functions of associated genes revealed that among primary biological processes enriched by genes under study are the processes of lipid metabolism, cellular interactions, various regulatory and transport processes in neural cells, processes of immune response regulation. Substantial part of investigated genes forms an interacting network, which consisted of distinct clusters corresponding to major biological processes, were genes under study are involved, and to basic molecular functions of their products. Data obtained in the project, extend the understanding of genetic component in neuro-psychiatric diseases, as well as the biological processes and functions, implemented in the manifestation of genetic susceptibility to AD and SZ.

Momelotinib Therapy in Myelofibrosis: 6-Years Follow-up Data on Safety, Efficacy and the Impact of Mutations on Overall and Relapse-Free Survival

Background:Momelotinib is a JAK 1/2 inhibitor that is active in the treatment of myelofibrosis (MF); a previous phase 1/2 study included 100 consecutive patients from the Mayo Clinic (Leukemia. 2015;29:741). In the current long-term study of these 100 patients, we provide a cumulative account of short and long term efficacy and toxicity data, as well as survival analysis.Methods:The current study represents sponsor-independent analysis. The study patients are part of a larger (n=166) phase-1/2 momelotinib study (NCT00935987), which was conducted in two dose-escalation (100 mg-400 mg daily doses) and dose-confirmation (300 mg daily dose) phases. Adverse events (AEs) were monitored by Common Terminology Criteria for Adverse Events (Version 4.03) and responses by the International Working Group criteria (Blood. 2013;122:1395). All statistical analyses considered clinical and laboratory parameters obtained at the time of entry to study.Results:Baseline data: 100 patients with MF (median age 66 years; 58% males) were treated between 11/20/09 and 11/10/10; 64 patients had primary MF, 22 post-polycythemia vera MF and 14 post-essential thrombocythemia MF. 73 (73%) patients harbored JAK2 mutations, 16 (16%) CALR, 7 MPL and 4 were "triple-negative"; among the 16 CALR-mutated cases, 13 were classified as "type 1/type 1-like". DIPSS-plus risk distribution (JCO 2011;29:392) was 63% high, 36% intermediate-2 and 1% intermediate-1; 49% displayed red cell transfusion-dependency, 58% constitutional symptoms, 87% palpable splenomegaly >5 cm and 50% abnormal karyotype. 94 patients were screened for ASXL1 mutations with 41 (44%) mutated and 78 for SRSF2 mutations with 14 (18%) mutated. 21 (21%) patients were previously treated with another JAK inhibitor.Current disposition: All information was updated in July 2016. To-date, after a median follow-up of 3.2 years, 88 drug discontinuations, 70 deaths and 14 leukemic transformations have been documented; median follow-up for living patients was 5.7 years (range 5.1-6.4). Among the 30 patients who are currently alive, 12 remain on study and another 5 have received stem cell transplant.Toxicity data: After a median treatment duration of 1.7 years, "momelotinib related" grade 3 or 4 AEs included thrombocytopenia (34%), neutropenia (9%), anemia (5%), increased lipase (7%), increased ALT (4%), increased AST (2%), increased ALP (2%) and headaches (2%). In addition, noteworthy grade 1 or 2 AEs included peripheral neuropathy (PN) 47%, increased lipase (14%), increased amylase (17%), increased bilirubin (13%), increased AST (21%), increased ALT (19%), increased APTT (17%), headaches (13%), dizziness (22%), nausea (23%) and diarrhea (20%). Most of the AEs, except PN, were reversible.Efficacy data and predictors of response and relapse-free survival: Clinical improvement (CI) was documented in 57% of patients, anemia response in 44%, and spleen response in 43%. 51% of transfusion-dependent patients became transfusion independent. The majority of patients also had marked improvement in their symptoms. 46 (81%) of the 57 responding patients discontinued treatment after a median treatment duration of 2.3 years. ASXL1 mutations predicted inferior CI (p=0.03) whereas relapse-free survival was adversely affected by absence of type 1/type 1-like CALR (p=0.03) or presence of unfavorable karyotype (p=0.002); among the 11 responding patients currently still receiving the drug, all had favorable karyotype and 5 had type 1/type 1-like CALR mutations.Survival analysis and risk factors: Median survival, calculated from the time of study entry, was 3.2 years with 5-year survival rate of 32%. In multivariable analysis of genetic markers, absence of type 1/type 1-like CALR (HR 2.9, 95% CI 1.1-7.2) or presence of SRSF2 (2.9, 1.5-5.4) or ASXL1 (1.8, 1.1-3.2) mutations were independently predictive of shortened survival (Figure).Conclusions:Momelotinib therapy in MF provides effective palliation in terms of anemia, splenomegaly and constitutional symptoms. However, less than 20% of treated patients enjoy durable long-term benefit and almost half experience drug-related and mostly irreversible peripheral neuropathy. Long-term survival and durability of response were superior in patients with type 1/type 1-like CALR mutations and inferior in those with ASXL1/SRSF2 mutations or unfavorable karyotype. [Display omitted] DisclosuresAl-Kali:Onconova Therapeutics, Inc.: Research Funding; Celgene: Research Funding.

Use of next-generation molecular tools in archaeological neotropical deer sample analysis

Taxonomic identity and genetic variation of three bone samples from a late Holocene earth mound in the eastern Uruguayan lowlands were analyzed. Samples were initially identified by morphology as being from pampas deer (Ozotoceros bezoarticus), a middle-sized cervid that occupies open environments forming herds of up to 50 animals. Prehistoric human communities may have developed herd management systems for this species. The aim of this study was to evaluate usefulness of a Next Generation Sequencing (NGS) strategy using pooled samples to explore genetic relationships between specimens. Two mitochondrial D-loop haplotypes were found which surprisingly identifies another deer species (Mazama gouazoubira). Our findings confirm that NGS is a powerful tool for taxonomic identification of ancient Uruguayan samples, also indicating that M. gouazoubira may be underrepresented in the zooarchaeological record of eastern Uruguay. Finally, since both species have different niches and behaviors it is necessary to formulate new questions in order to understand prehistoric management of Neotropical deer involving larger sample sizes and analysis of other genetic markers.

More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing.

BackgroundAlthough the primary objective of forensic DNA analyses of unidentified human remains is positive identification, cases involving historical or archaeological skeletal remains often lack reference samples for comparison. Massively parallel sequencing (MPS) offers an opportunity to provide biometric data in such cases, and these cases provide valuable data on the feasibility of applying MPS for characterization of modern forensic casework samples. In this study, MPS was used to characterize 140-year-old human skeletal remains discovered at a historical site in Deadwood, South Dakota, United States. The remains were in an unmarked grave and there were no records or other metadata available regarding the identity of the individual. Due to the high throughput of MPS, a variety of biometric markers could be typed using a single sample.ResultsUsing MPS and suitable forensic genetic markers, more relevant information could be obtained from a limited quantity and quality sample. Results were obtained for 25/26 Y-STRs, 34/34 Y SNPs, 166/166 ancestry-informative SNPs, 24/24 phenotype-informative SNPs, 102/102 human identity SNPs, 27/29 autosomal STRs (plus amelogenin), and 4/8 X-STRs (as well as ten regions of mtDNA). The Y-chromosome (Y-STR, Y-SNP) and mtDNA profiles of the unidentified skeletal remains are consistent with the R1b and H1 haplogroups, respectively. Both of these haplogroups are the most common haplogroups in Western Europe. Ancestry-informative SNP analysis also supported European ancestry. The genetic results are consistent with anthropological findings that the remains belong to a male of European ancestry (Caucasian). Phenotype-informative SNP data provided strong support that the individual had light red hair and brown eyes.ConclusionsThis study is among the first to genetically characterize historical human remains with forensic genetic marker kits specifically designed for MPS. The outcome demonstrates that substantially more genetic information can be obtained from the same initial quantities of DNA as that of current CE-based analyses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3087-2) contains supplementary material, which is available to authorized users.