Minor Mutations Research Articles

Abstract 3584: Analysis of colorectal intratumoral genetic heterogeneity by high efficiency and rapid deep targeted sequencing

Abstract Metastasis is the most frequent cause of morbidity and mortality in cancer. Metastatic disease lethality is often the result of cancer progression despite treatment. Therapeutic resistance is seen nearly in all cases of metastatic cancer. Genetic studies relying on deep sequencing have shown that many cancers are genetically heterogeneous as a result of diverse clonal populations with delineating and unique set of mutations. Several studies suggest that resistance mutations are present in tumors before the start of treatment and via evolution, clonal populations expand under therapeutic selection. However, these minor allelic mutations that define clonal populations are not typically detectable with typical sequencing coverage (20-50X) employed in whole genome approaches. Relying on an innovative programmable targeting method that enables us to rapidly configure nearly any region of the human genome and efficiently sequence cancer genomes, we are determining the extent of intratumoral genetic heterogeneity and clonal diversity in colorectal cancer. Our study involves over 120 patients with available clinical data and a subset of matched tumors indicative of tumor progression (e.g. tumor-normal, premalignant-malignant, malignant-metastasis). Via an integrative analysis of TCGA, COSMIC and other genomic data sets of colorectal cancer, we identified the top ranking 53 cancer genes prone to mutation and associated with advanced colorectal cancer by. These top genes are found in known cancer pathways such as the WNT and RAS/RAF pathway and we are analyzing the exons of these genes for mutations, insertions and deletions with a sequencing depth of at least 1000x. Preliminary results have shown that we can readily reach sequencing depths of 7000x with our automated targeting approach and that a minimal sequencing depth of 1000x will enable detection of aberrations present in the sample below 1%. Samples are being analyzed for the overall level of heterogeneity and correlation of clonal mutations to clinical outcome. For optimal personalized treatment of cancer patients, the analysis of intratumoral genetic heterogeneity may be useful in predicting treatment response and metastatic potential of any given primary colorectal cancer. Citation Format: Erik S. Hopmans, Hojoon Lee, Laura Miotke, Rowza Tur Rumma, Sue Grimes, John M. Bell, Hanlee P. Ji. Analysis of colorectal intratumoral genetic heterogeneity by high efficiency and rapid deep targeted sequencing. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3584. doi:10.1158/1538-7445.AM2014-3584

No syntax saltation in language evolution

Much of the recent literature within the Minimalist/biolinguistic paradigm argues that the core language faculty, or more specifically ‘narrow syntax’, arose abruptly and rather recently, certainly within the last 100,000 years. The proposed syntax saltation is taken to be the result of a minor mutation, giving rise to the Merge operation which creates hierarchical structures. Moreover, externalization – using language for communication – is claimed to be a development subsequent to the use of language purely for internal thought. I argue against these claims, both on language-internal grounds, using evidence from the lexicon and from syntactic displacement, and on the basis of the archaeological findings.

209P - Clinical Validation of a Novel Multiplex Kit for All Ras Mutations in Colorectal Cancer: Results of Rasket(Ras Key Testing) Prospective Multicenter Study

Abstract Background RAS ( KRAS and NRAS ) testing is required to predict anti-epidermal growth factor receptor (EGFR) treatment efficacy in metastatic colorectal cancer (CRC). Although direct sequencing (DS) with manual microdissection (MMD) is widely used, a diagnostic kit providing rapid detections of RAS mutations would be clinically beneficial. We evaluated the MEBGEN TM RASKET KIT (RASKET KIT), a multiplex assay using PCR-reverse sequence specific oligonucleotide and xMAP ® technology to concurrently detect exon 2, 3, and 4 RAS mutations in a short turnaround time (4.5h/96-specimens). Methods Formalin-fixed paraffin-embedded (FFPE) tissues were obtained from 308 consenting patients with histologically-confirmed CRC at six hospitals in Japan. For the RASKET KIT, we used only 50–100ng DNA from each FFPE specimen not processed by MMD. The primary endpoint was the concordance rate between RAS mutations identified with the RASKET KIT and two reference assays (DS with MMD and TheraScreen ® K-RAS Mutation Kit). As the secondary endpoints, we evaluated the concordance rate between DS and the RASKET KIT for RAS mutations in the wild-type KRAS exon 2 population and the genotyping performance of the RASKET KIT compared with DS. Findings Among 307 analyzable specimens, the reference assays detected 140 (45.6%, 140/307) RAS mutations: 111 KRAS exon 2 and 29 other (minor) RAS mutations. The RASKET KIT detected 143 (46.6%, 143/307) mutations: 114 KRAS exon 2 and 29 minor RAS mutations. The between-method concordance rate was 96.7% (297/307) (95% CI: 94.1–98.4%). Minor RAS mutations were detected in 15.7% (30/191) of the wild-type KRAS exon 2 population ( n =191); the concordance rate was 98.4% (188/191) (95% CI: 95.5–99.7%). The concordance rate of RAS genotyping was 100% (139/139) (95% CI: 97–100%). Interpretation The RASKET KIT provides rapid and precise detections of RAS mutations and consequently, quicker and more effective anti-EGFR therapy for CRC (Study ID: UMIN000011784). Funding Medical & Biological Laboratories Co., Ltd. (MBL). MBL had roles in study design, data collection, data analysis, and writing of the report for the study.

Low concordance and resistance mutation emergence in the HIV protease gene among circulating and cell-associated viruses at viral replication episodes during darunavir/ritonavir monotherapy.

To assess the changes on the HIV protease gene in plasma and peripheral blood mononuclear cell (PBMC) compartments during viral replication episodes in patients on boosted-darunavir monotherapy (mtDRV/rtv). A prospective study was carried out in which adult HIV-1-infected patients who started mtDRV/rtv after viral suppression for ≥ 6 months with no major darunavir-related resistance mutations were enrolled. Patients with two consecutive plasma HIV RNA measurements >200 HIV-1 RNA copies/mL were considered as having virological failure (VF), while patients with two consecutive plasma HIV RNA measurements >50 copies/mL without meeting the VF criteria were considered to have virological rebound (VR). HIV protease genotypic profiles from plasma and PBMCs were performed at baseline and at VF and VR episodes. One hundred and fifty patients were included in the study, with overall VF and VR rates of 14% (n=21) and 14.7% (n=22), respectively. No major darunavir resistance mutations were observed in the plasma or PBMC samples. Circulating and cell-associated viruses showed a wild-type protease gene sequence in 54% and 23% of patients, respectively while the remainder patients only harboured minor protease inhibitor-associated mutations. Full concordance between plasma RNA and PBMC DNA protease genotypes was found in 23% of the sequences. No darunavir-related mutations were found in patients with VF or VR, either in plasma or in PBMCs; thus, simplification to mtDRV/rtv does not comprise future antiretroviral treatment options.

Comparison of ultra-deep versus Sanger sequencing detection of minority mutations on the HIV-1 drug resistance interpretations after virological failure

Drug-resistance mutations are routinely detected using standard Sanger sequencing, which does not detect minor variants with a frequency below 20%. The impact of detecting minor variants generated by ultra-deep sequencing (UDS) on HIV drug-resistance interpretations has not yet been studied. Fifty HIV-1 patients who experienced virological failure were included in this retrospective study. The HIV-1 UDS protocol allowed the detection and quantification of HIV-1 protease and reverse transcriptase variants related to genotypes A, B, C, F and G. DeepChek-HIV simplified drug-resistance interpretation software was used to compare Sanger sequencing and UDS. The total time required for the UDS protocol was found to be approximately three times longer than Sanger sequencing with equivalent reagent costs. UDS detected all of the mutations found by population sequencing and identified additional resistance variants in all patients. An analysis of drug resistance revealed a total of 643 and 224 clinically relevant mutations by UDS and Sanger sequencing, respectively. Three resistance mutations with more than 20% prevalence were detected solely by UDS: A98S (23%), E138A (21%) and V179I (25%). A significant difference in the drug-resistance interpretations for 19 antiretroviral drugs was observed between the UDS and Sanger sequencing methods. Y181C and T215Y were the most frequent mutations associated with interpretation differences. A combination of UDS and DeepChek software for the interpretation of drug resistance results would help clinicians provide suitable treatments. A cut-off of 1% allowed a better characterization of the viral population by identifying additional resistance mutations and improving the drug-resistance interpretation.

Presence of the minor EGFR T790M mutation is associated with drug-sensitive EGFR mutations in lung adenocarcinoma patients.

The T790M mutation in the epidermal growth factor receptor (EGFR) gene is known to be associated with the acquired resistance of lung adenocarcinoma patients to EGFR-tyrosine kinase inhibitors (EGFR-TKIs). The minor T790M mutant allele is occasionally detected in EGFR-TKI-naive tumor samples, yet findings concerning the clinical impact of the minor T790M mutation vary among previous studies. In the present study, we assessed the clinical impact of the minor T790M mutation using a novel, highly sensitive assay combining high-resolution melting (HRM), mutant-enriched PCR and co-amplification at a lower denaturation temperature (COLD)-PCR. We determined the T790M mutational status in 146 surgically resected lung adenocarcinomas without a history of EGFR-TKI treatment using mutant-enriched COLD-HRM (MEC-HRM) and standard HRM assays. The sensitivities of the MEC-HRM and standard HRM assays for the detection of T790M-mutant alleles among wild-type alleles were 0.01 and 10%, respectively. Although the T790M mutation was not detected using a standard HRM assay, we identified 19 (13%) T790M mutations using the MEC-HRM assay and defined these 19 mutations as minor T790M mutations. The proportion of T790M alleles was <0.1% in 17 (84%) of the 19 samples. Multivariate analyses revealed that a minor T790M mutation was significantly associated with the presence of EGFR exon 19 deletions or the L858R mutation (both of which are drug-sensitive EGFR mutations) (P=0.04). In conclusion, the minor EGFR T790M mutations were present in 13% of EGFR-TKI-naive surgically resected lung adenocarcinomas and were associated with drug-sensitive EGFR mutations.

HIV drug resistance in newly diagnosed adults in a rural prefecture of eastern China.

Little is known about HIV drug resistance (HIVDR) in newly diagnosed HIV-infected adults in eastern China where the HIV epidemic is spreading predominantly through sexual contact. During 2008-2011, newly HIV-diagnosed adults in Taizhou prefecture, Zhejiang province in eastern China were examined for HIVDR by amplifying and sequencing the HIV-1 pol gene. Of 447 genotyped participants, 53·7% were infected with CRF01_AE, 20·1% with CRF07_BC, 12·5% with subtype B, and 11·6% with CRF08_BC. Most of the participants had one or more minor genetic mutations in the pol gene that are associated with HIVDR. Twelve (2·7%) participants met the standard guidelines of having low to high HIVDR, suggesting that the prevalence of HIVDR in newly HIV-diagnosed adults was low in the study area and current antiretroviral therapy (ART) regimens are likely to remain effective. However, given high frequency of minor HIVDR in HIV patients and the scaling up of ART programmes in China, larger HIVDR surveillance programmes are needed.

Clinical impact of ultra deep versus Sanger sequencing detection of minority mutations on HIV-1 drug resistance genotype interpretation after virological failure

Methods Fifty HIV-1 patients who experienced virological failure were included in this retrospective study. The HIV-1 UDS protocol was performed using the GS Junior (Roche 454 Life Sciences Branford, CT). This UDS protocol allowed the detection and quantification of minor and major HIV-1 protease and reverse transcriptase variants related to genotypes A, B, C, E, F and G. DeepChekHIV (ABL, SA and TherapyEdgeTM, USA) simplified drug resistance (DR) interpretation software was used to compare Sanger sequencing and UDS at two different thresholds (≥1% and ≥20%). DeepChek-HIV utilizes the ANRS, HIVdb and Rega algorithms.

Molecular characterization of circulating pandemic strains of influenza A virus during 2012 to 2013 in Lucknow (India).

The pandemic H1N1 strain of Influenza A virus [A(H1N1)pdm09] is now well adapted in human populations. However, it is still causing sporadic outbreaks worldwide with different severity. The present study was planned to understand the genetic diversity (based on the HA1 gene) of influenza A(H1N1)pdm09 strains circulating during the post pandemic period. The HA1 gene was selected because the HA1 protein is immunogenic, functions as a receptor binding site and indirectly affects transmission and pathogenicity of virus. A total of 2,818 cases were enrolled. Nasal/throat swabs from all cases were tested by one-step real time PCR for detection of influenza virus types and subtypes according to the CDC protocol. Of these, 134 cases were A(H1N1)pdm09 positive, 34 of which were screened for HA1 gene (position 434-905) sequencing (Big-Dye terminator using 3130 ABI, Genetic analyzer). Molecular and phylogenetic analysis was performed using PhyML approach (v. 3.0). All A(H1N1)pdm09 positive and negative cases were clinically characterized. Phylogentically, all Lucknow strains (n = 33) except one fall with the clade seven reference strain. One strain showed 99.9% similarities with clade one reference strain A/California/07/2009. In mutational analysis, 33 strains had the S220T mutation, which is at an antigenic site and characteristic of clade seven along with few minor mutations; K180I/T/Q, V190I, S200P, S202T, A203T, A214T, S220T, V251I, and A273T. These results suggest that clade seven was the most widely circulating clade in Lucknow and A(H1N1)pdm09 cases showed mild clinical symptoms as compared to A(H3N2) or influenza B cases.

An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing

The detection of mutant spectra within the viral quasispecies is critical for therapeutic management of HIV-1 infections. Routine clinical application of ultrasensitive genotyping requires reproducibility and concordance within and between laboratories. The goal of the study was to evaluate a new protocol on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing (454-UDS) in an international multicenter study. Sixteen blinded HIV-1 subtype B samples were provided for 454-UDS as both RNA and cDNA with viral titers of 88,600–573,000 HIV-1 RNA copies/ml. Eight overlapping amplicons spanning protease (PR) codons 10–99 and reverse transcriptase (RT) codons 1–251 were generated using molecular barcoded primers. 454-UDS was performed using the 454 Life Sciences/Roche GS FLX platform. PR and RT sequences were analyzed using 454 Life Sciences Amplicon Variant Analyzer (AVA) software. Quantified variation data were analyzed for intra-laboratory reproducibility and inter-laboratory concordance. Routine population sequencing was performed using the ViroSeq HIV-1 genotyping system. Eleven laboratories and the reference laboratory 454 Life Sciences sequenced the HIV-1 sample set. Data presented are derived from seven laboratories and the reference laboratory since severe study protocol execution errors occurred in four laboratories leading to exclusion. The median sequencing depth across all sites was 1364 reads per position (IQR=809–2065). 100% of the ViroSeq-reported mutations were also detected by 454-UDS. Minority HIV-1 drug resistance mutations, defined as HIV-1 drug resistance mutations identified at frequencies of 1–25%, were only detected by 454-UDS. Analysis of 10 preselected majority and minority mutations were consistently found across sites. The analysis of drug-resistance mutations detected between 1 and 10% demonstrated high intra- and inter-laboratory consistency in frequency estimates for both RNA and prepared cDNA samples, indicating robustness of the method. HIV-1 drug resistance testing using 454 ultra-deep pyrosequencing results in an accurate and highly reproducible, albeit complex, approach to the analysis of HIV-1 mutant spectra, even at frequencies well below those detected by routine population sequencing.

At the Edge of Chaos?: Foreign Investment Law as a Complex Adaptive System, How It Emerged and How It Can Be Reformed

Foreign investment law (FIL) is unlike any other sub-field of international law. Its unique features continue to puzzle observers. Two general themes recur. First, why do countries agree to so substantially limit their sovereign powers over foreign investors and, most strikingly, to open themselves up to direct claims in investor-state arbitration? Second, how can FIL survive given its composition of thousands of treaties, custom, domestic laws, contracts and (often contradictory) arbitration awards, without a controlling multilateral treaty or institution, or appellate court? This article draws on complexity theory and the notion of complex adaptive systems to offer an alternative, richer account of FIL. Approaching FIL as a complex adaptive system (CAS) allows us to better understand how FIL (i) emerged out of small, incremental and often accidental steps, (ii) operates as a largely self-organizing, decentralized system made up of many interacting components and (iii) stabilizes but also changes and evolves through a series of local, sub-optimal quasi-equilibria, highly sensitive to initial conditions that can be disturbed by both seismic events or major crises and minor mutations. The insights thus provided should also help participants in FIL to develop interventions or reforms that are more likely to be effective, in casu relatively small tweaks or adaptations which may have major repercussions. Seeking the edge of chaos, therefore, is not seeking disorder or randomness but the right balance between order and flexibility. This perspective should give pause to lawyers, generally critical of fragmentation and decentralization, and intuitively in search of order and central authority. Through the lens of complexity theory, FIL, with all its imperfections, and contrary to conventional wisdom, may not be one of law’s most pathological sub-fields in need of top-to-bottom reform. Though far from optimal, it may be an organizational life form more similar to species that have survived evolutionary biology and, in this sense, be a model that other legal regimes may want to learn and copy from.

Hepatitis C virus NS3 mutations in haemophiliacs

Haemophiliacs have high hepatitis C virus (HCV) exposure risk from blood products that did not undergo heat inactivation or disease-specific screening prior to 1987. Repeated exposure to infected factor concentrates predisposes haemophiliacs to higher likelihood of HCV from multiple sources. HIV coinfection could result in impaired clearance of less fit variants resulting in enrichment of quasispecies carrying resistance mutations. We postulated that haemophiliacs demonstrate increased prevalence of baseline signature mutations in the HCV NS3/4 serine protease coding domain. We examined the prevalence of putative HCV protease inhibitor mutations, mutations, subclassified into dominant mutations if changes conferred resistance, and minor variants not associated with drug resistance, in patients with haemophilia A or B, infected with HCV or HCV/HIV, prior to HCV PI exposure. A total of 151 subjects were evaluated, including 22 haemophiliacs and 129 non-haemophilic controls. Of the 58 mutations detected, 55 (95%) were resistance mutations and three (5%) were minor variants. Dominant mutations were detected in 10 (45.5%) haemophiliacs and in 43 (33.3%) controls (OR 1.67, 95% CI 0.67-4.16). There was no statistical difference in proportion of dominant mutations (P=0.27) or minor variants (P=0.47) between groups, despite adjustment for HIV status (P=0.44). No significant differences in dominant or minor resistance mutations between haemophiliacs and non-haemophiliacs were observed. HIV presence or prior HAART exposure did not affect baseline distribution. We conclude that haemophiliacs are not at higher risk for pre-existing HCV PI mutations, and prospective studies of response to PI-based regimens with HCV activity are indicated.

Probability of antibody formation against circumsporozoite protein of Plasmodium vivax among Korean malaria patients.

To evaluate the seroprevalence against circumsporozoite protein (CSP) of Plasmodium vivax in sera of Korean patients, the central repeating domain (CRD) of CSP was cloned and analyzed. From the genomic DNA of patient's blood, 2 kinds of CSPs were identified to belong to a VK210 type, which is the dominant repeating of GDRA(D/A)GQPA, and named as PvCSPA and PvCSPB. Recombinantly expressed his-tagged PvCSPA or PvCSPB in Escherichia coli reacted well against sera of patients in western blot, with the detecting rate of 47.9% (58/121), which included 15 cases positive for PvCSPA, 6 cases positive for PvCSPB, and 37 cases for both. The mixture of PvCSPA and PvCSPB was loaded to a rapid diagnostic test kit (RDT) and applied with the same set of patient sera, which resulted in detection rates of 57.0% (69/121). When the protein sequences of PvCSPA were compared with those of P. vivax in endemic regions of India and Uganda, they were compatibly homologous to PvCSPA with minor mutations. These results suggested that the recombinant PvCSPA and PvCSPB loaded RDT may be a milestone in latent diagnosis which has been a hot issue of domestic malaria and important for radical therapy in overlapped infections with P. falciparum in tropical and subtropical areas. During the biological process of malarial infection, exposure of CSP to antigen-antibody reaction up to 57.0% is the first report in Korea.

Characteristics of HIV-1 Natural Drug Resistance-Associated Mutations in Former Paid Blood Donors in Henan Province, China

BackgroundNatural drug resistance is a major cause of antiviral treatment failure. The characteristics of HIV-1 natural drug resistance-associated mutations in former paid blood donors in Henan Province remain unclear.MethodsOne hundred and fifty HIV-1-positive plasma samples were collected. Plasma viral RNA was extracted for pol gene amplification and sequencing. The sequencing results were submitted to the HIV-1 drug resistance database for drug-resistance analysis.ResultsThe rates of natural drug resistance and resistance-associated mutations were 17.7% (19/107) and 40.2% (43/107), respectively. The rates of PI major, PI minor, NRTI, and NNRTI mutations were: 0, 30.8% (33/107), 10.3% (11/107), and 18.7% (20/107), respectively. Nine cases (8.4%) had both NRTI and NNRTI resistance-associated mutations. Seven cases (6.5%) had PI minor, NRTI and NNRTI resistance-associated mutations. NNRTI resistance was the most serious, followed by NRTI resistance and PI resistance. Polymorphism mutation sites with mutation rates in the protease region higher than 60.0% were: L63A/P/S/T 89.7%, V77I 82.2%, I72E/M/K/T/V 80.4%, I93L 75.7%, and E35D 72.9%. Polymorphism mutation sites with mutation rates in the RT region higher than 60.0% were: I135A/L/M/R/T/V 93.5%, T200A/E/I/P/V 89.7%, Q278E/K/N/T 88.8%, S162C/Y 82.2%, and K277R/S 66.4%. The distribution of 107 gene sequences was scattered, with some drug-resistant strains grouped in the same cluster.ConclusionThe natural drug resistance mutation rate of HIV-1 in former paid blood donors in Henan Province was 17.7%, with NNRTI resistance the most serious. The distribution of drug-resistant strains was scattered, with some correlations found in certain resistance loci.

H63D Genotying for Hemochromatosis: Helper or Hindrance?

H63D Genotying for Hemochromatosis: Helper or Hindrance?

Naturally occurring protease inhibitor resistance mutations and their frequencies in HIV proviral sequences of drug-naïve sex workers in Nairobi, Kenya

Sub-Saharan Africa accounts for 69% of the people living with HIV globally. An estimated 1,600,000 Kenyans are living with HIV-1. Antiretroviral therapy (ART) has saved 9 million life-years in Sub-Saharan Africa. However, drug resistance mutations reduce the effectiveness of ART, and need to be monitored for effective ART. Naturally occurring primary antiretroviral drug resistance mutations have not been well analyzed in ART naive HIV+ patients in Kenya. Here we have examined protease inhibitor (PI) resistance mutations in ART naive HIV-1 seropositive women in Pumwani sex worker cohort established in Nairobi, Kenya, wherein HIV-1 infection is predominantly caused by subtypes A and D viruses. We have analyzed consensus sequences of HIV protease from 109 drug-naive patients, as a part of HIV-1 whole-genome sequencing using 454 sequencing methodology. Analysis using HIVdb program revealed a prevalence of 22% (24/109) PI resistance mutations among the study subjects. D30N (3.7%), M46I (0.9%) and V82F (0.9%) are the major mutations observed. D30N mutation is known to confer high-level resistance to nelfinavir. M46I and V82F confer resistance to indinavir, lopinavir, fosamprenavir and nelfinavir. In addition, many minor mutations were found at seven different drug resistance sites. It is important to study the implications of these mutations to the effectiveness of specific PI drug treatment. This study provides valuable data pertaining to primary drug resistance in Kenyan HIV-1 infected patients before ART became available.

Invasive toxic prey may imperil the survival of an iconic giant lizard, the Komodo dragon.

Although invasive species constitute a major threat to global biodiversity, the introduction of toxic prey into naïve predator faunas may become particularly destructive. An example of such an introduction was the deliberate release of the highly toxic cane toad (Bufo marinus) to the toad-free Australian continent in 1935. Naïve large Australian varanid lizards have recently been shown to suffer a massive increase in mortality (&gt; 95%) when attempting to feed on this toxic amphibian. The high susceptibility of Australian varanids to toad toxin is caused by minor mutations in the sodiumpotassium- ATPase enzyme. In the present study we show that Komodo dragons (Varanus komodoensis) have similar mutations within this enzyme as observed in Australian varanids demonstrating that dragons are extremely susceptible to toad toxin. During the last decade the black-spined toad (Bufo melanostictus) has been able to invade areas close to the five toad-free islands constituting the habitat of Komodo dragons. An invasion of highly toxic black-spined toads into dragon habitats may therefore cause similar dramatic increase in dragon mortality as recorded in Australian varanids imperiling the long-term survival of this giant and iconic lizard.

Quantitative Transmitted Drug Resistance (TDR) Variation in Acute/Recently Infected Men who have Sex with Men (MSM) Chinese HIV Patient Cohort

Transmitted drug resistance (TDR) is an ongoing public health problem in HIV disease treatment and increases the risk of virologic failure following combination anti-retroviral therapy (cART) initiation. Current HIV treatment guidelines recommend resistance testing at entry into HIV care and at cART initiation. In this study, we longitudinally observed 10 acute/recently infected patients for 24-51 months. In addition to calculating the replacement rate of TDR measured by bulk population sequencing, High-throughput sequencing (HTS) was used to detect the minority mutations and quantify the variation of each TDR mutations during the follow-up. We compared the predictions of virus sensitivity to each drug by bulk population sequencing alone or by the combined sequencing with bulk population sequencing and HTS, which was analyzed with their virologic response after 6 months antiretroviral therapy. Our observations provided insights into the significance of low-frequency HIV-1 drug resistance mutations in acute/recently infected patients, and whether or not TDR are likely to revert, or persist as minority species or be stable. This study not only provides valuable data on TDR prevalence but also has important implications for the clinical management of these patients.

Analysis of HIV-1 drug resistance in Gulf countries

Introduction HIV/AIDS is a major health concern towards global population. The Arabian Peninsula consists of seven countries, as Gulf Cooperation Council (GCC) which is considered to be part of Middle East. According to the 2012 estimates for Middle East the estimated number of people acquiring HIV rose by more than 50%. The first AIDS case in a Saudi Arabian individual was reported in 1984 and since then, the number has been increasing. Patients are administered with antiretroviral therapy that reduces morbidity and mortality associated with HIV infection. Due to selective pressure from these antiretroviral drugs, the virus develops mutations for this purpose and up to date data regarding the prevalence of drug resistance mutations is required. Objective To determine HIV drug resistance in GCC countries using bioinformatics tools. Materials and method Available pol sequences of Saudi Arabia, Kuwait and Yemen were retrieved from Los Alamos database and entered into Stanford HIV Database from which data for drug resistance and mutations were analyzed. Results 11% of the Saudi Arabian sequences showed low level resistance in virus. However 26% of prot sequences from Yemen showed minor mutations and 5% showed minor mutation for rt. 15% sequences for Kuwait prot region showed minor mutations and 14% in rt region showed minor mutation causing low to potentially low level resistance. Conclusion Majority of the sequences from the GCC countries showed minor mutations but no major mutation is seen against the virus. The data suggest that infection is new in the region, thus virus is still sensitive to most of the drugs.

Networks of lexical borrowing and lateral gene transfer in language and genome evolution.

Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution.