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Supplementary Table 2 from A Segregation Analysis of Barrett's Esophagus and Associated Adenocarcinomas

Familial aggregation of esophageal adenocarcinomas, esophagogastric junction adenocarcinomas, and their precursor Barrett's esophagus (BE) has been termed familial BE (FBE). Numerous studies documenting increased familial risk for these diseases raise the hypothesis that there may be an inherited susceptibility to the development of BE and its associated cancers. In this study, using segregation analysis for a binary trait as implemented in S.A.G.E. 6.0.1, we analyzed data on 881 singly ascertained pedigrees to determine whether FBE is caused by a common environmental or genetic agent and, if genetic, to identify the mode of inheritance of FBE. The inheritance models were compared by likelihood ratio tests and Akaike's A Information Criterion. Results indicated that random environmental and/or multifactorial components were insufficient to fully explain the familial nature of FBE, but rather, there is segregation of a major type transmitted from one generation to the next (P < 10−10). An incompletely dominant inheritance model together with a polygenic component fits the data best. For this dominant model, the estimated penetrance of the dominant allele is 0.1005 [95% confidence interval (95% CI), 0.0587-0.1667] and the sporadic rate is 0.0012 (95% CI, 0.0004-0.0042), corresponding to a relative risk of 82.53 (95% CI, 28.70-237.35) or odds ratio of 91.63 (95% CI, 32.01-262.29). This segregation analysis provides epidemiologic evidence in support of one or more rare autosomally inherited dominant susceptibility allele(s) in FBE families and, hence, motivates linkage analyses. Cancer Epidemiol Biomarkers Prev; 19(3); 666–74

PDF file, 102K, Linkage locations suggested by Loki on chromosome 17 by batches of 100K iterations and over all 500K iterations.

Supplementary Table 3 from A Segregation Analysis of Barrett's Esophagus and Associated Adenocarcinomas

PDF file, 212K, Genome-wide multipoint model-based linkage under the three trait locus segregation models. Multipoint LOD scores have been truncated at -3. Some scores are below -3, such as for the whole of chromosome 15.

PDF file, 302K, Scatter plot of the visits at possible linked QTL locations on chromosome 17 vs. iteration.

PDF file, 133K, Additional methods describing the segregation-linkage analysis approach with variable age at onset.

PDF file, 89K, L-scores for three prior settings, after discarding the beginning 5K iterations

PDF file, 34K, Typical assumptions in model-based vs. model-free multipoint linkage analysis.

Genetic risk factors are important contributors to the development of colorectal cancer. Following the definition of a linkage signal at 9q22-31, we fine mapped this region in an independent collection of colon cancer families. We used a custom array of single-nucleotide polymorphisms (SNP) densely spaced across the candidate region, performing both single-SNP and moving-window association analyses to identify a colon neoplasia risk haplotype. Through this approach, we isolated the association effect to a five-SNP haplotype centered at 98.15 Mb on chromosome 9q. This haplotype is in strong linkage disequilibrium with the haplotype block containing HABP4 and may be a surrogate for the effect of this CD30 Ki-1 antigen. It is also in close proximity to GALNT12, also recently shown to be altered in colon tumors. We used a predictive modeling algorithm to show the contribution of this risk haplotype and surrounding candidate genes in distinguishing between colon cancer cases and healthy controls. The ability to replicate this finding, the strength of the haplotype association (odds ratio, 3.68), and the accuracy of our prediction model (∼60%) all strongly support the presence of a locus for familial colon cancer on chromosome 9q. Cancer Res; 70(13); 5409–18. ©2010 AACR.

Supplementary Table 1 from Confirmation of Linkage to and Localization of Familial Colon Cancer Risk Haplotype on Chromosome 9q22

GSK3389404, an N-acetyl galactosamine-conjugated antisense oligonucleotide (ASO), was in clinical development for chronic hepatitis B (CHB) treatment. Few studies have examined ASOs in Asian participants. In this analysis, the plasma pharmacokinetics (PK) of GSK3389404 were characterized and compared in patients with CHB across the Asia-Pacific region (N = 64), including mainland China (

Chronic infection with hepatitis B virus (HBV) leads to an increased risk of death from cirrhosis and hepatocellular carcinoma. Functional cure rates are low with current treatment options (nucleos(t)ide analogs (NAs) and pegylated interferons). Bepirovirsen is an antisense oligonucleotide targeting all HBV messenger RNAs; in cell culture and animal models, bepirovirsen leads to reductions in HBV-derived RNAs, HBV DNA and viral proteins. This phase 2 double-blinded, randomized, placebo-controlled trial is the first evaluation of the safety and activity of an antisense oligonucleotide targeting HBV RNA in both treatment-naïve and virally suppressed individuals with chronic HBV infection. The primary objective was to assess the safety and tolerability of bepirovirsen in individuals with chronic hepatitis B (CHB) (NCT02981602). The secondary objective was to assess antiviral activity, including the change from baseline to day 29 in serum hepatitis B surface antigen (HBsAg) concentration. Participants with CHB infection ≥6 months and serum HBsAg ≥50 IU ml−1 were enrolled from seven centers across Hong Kong and the Republic of Korea and randomized (3:1 within each dose cohort) to receive bepirovirsen or placebo via subcutaneous injection twice weekly during weeks 1 and 2 (days 1, 4, 8 and 11) and once weekly during weeks 3 and 4 (days 15 and 22). Participants were then followed for 26 weeks. Twenty-four participants were treatment-naïve and seven were receiving stable NA therapy. Treatment-emergent adverse events were mostly mild/moderate (most commonly injection site reactions). Eleven (61.1%) and three (50.0%) treatment-naïve participants experienced one or more treatment-emergent adverse event in the bepirovirsen and placebo groups, respectively. In participants receiving NA therapy, the corresponding numbers were three (60.0%) and one (50.0%). Transient, self-resolving alanine aminotransferase flares (≥2× upper limit of normal) were observed in eight treatment-naïve participants and three participants on stable NA regimens in the bepirovirsen treatment arms. HBsAg reductions were observed and were significant versus placebo for treatment-naïve participants receiving bepirovirsen 300 mg (P = 0.001), but not for the bepirovirsen 150 mg group (P = 0.245) or participants receiving stable NA therapy (P = 0.762). Two participants in each of the 300 mg dose groups achieved HBsAg levels below the lower limit of quantitation by day 29 (n = 3) or day 36 (n = 1). Bepirovirsen had a favorable safety profile. These preliminary observations warrant further investigation of the safety and activity of bepirovirsen in a larger CHB patient population., A first-in-human study of an antisense oligonucleotide targeting hepatitis B virus (HBV) RNA provides initial insights into this potential new therapeutic modality for individuals with chronic HBV infection.

Background Bepirovirsen is an antisense oligonucleotide that targets all hepatitis B virus (HBV) messenger RNAs and acts to decrease levels of viral proteins. Methods We conducted a phase 2b, randomized, investigator-unblinded trial involving participants with chronic HBV infection who were receiving or not receiving nucleoside or nucleotide analogue (NA) therapy. Participants were randomly assigned (in a 3:3:3:1 ratio) to receive weekly subcutaneous injections of bepirovirsen at a dose of 300 mg for 24 weeks (group 1), bepirovirsen at a dose of 300 mg for 12 weeks then 150 mg for 12 weeks (group 2), bepirovirsen at a dose of 300 mg for 12 weeks then placebo for 12 weeks (group 3), or placebo for 12 weeks then bepirovirsen at a dose of 300 mg for 12 weeks (group 4). Groups 1, 2, and 3 received loading doses of bepirovirsen. The composite primary outcome was a hepatitis B surface antigen (HBsAg) level below the limit of detection and an HBV DNA level below the limit of quantification maintained for 24 weeks after the planned end of bepirovirsen treatment, without newly initiated antiviral medication. Results The intention-to-treat population comprised 457 participants (227 receiving NA therapy and 230 not receiving NA therapy). Among those receiving NA therapy, a primary-outcome event occurred in 6 participants (9%; 95% credible interval, 0 to 31) in group 1, in 6 (9%; 95% credible interval, 0 to 43) in group 2, in 2 (3%; 95% credible interval, 0 to 16) in group 3, and 0 (0%; post hoc credible interval, 0 to 8) in group 4. Among participants not receiving NA therapy, a primary-outcome event occurred in 7 participants (10%; 95% credible interval, 0 to 38), 4 (6%; 95% credible interval, 0 to 25), 1 (1%; post hoc credible interval, 0 to 6), and 0 (0%; post hoc credible interval, 0 to 8), respectively. During weeks 1 through 12, adverse events, including injection-site reactions, pyrexia, fatigue, and increased alanine aminotransferase levels, were more common with bepirovirsen (groups 1, 2, and 3) than with placebo (group 4). Conclusions In this phase 2b trial, bepirovirsen at a dose of 300 mg per week for 24 weeks resulted in sustained HBsAg and HBV DNA loss in 9 to 10% of participants with chronic HBV infection. Larger and longer trials are required to assess the efficacy and safety of bepirovirsen. (Funded by GSK; B-Clear ClinicalTrials.gov number, NCT04449029.)

Bepirovirsen, an antisense oligonucleotide targeting pregenomic and mRNA transcripts of HBV, has been conjugated to N-acetyl galactosamine (GSK3389404) to enhance hepatocyte delivery. This dose-finding study was the first to assess GSK3389404 for chronic HBV infection.This phase IIa, randomised, double-blind, placebo-controlled, 2-part study was conducted in 22 centres in Asia (NCT03020745). Pharmacokinetic findings from Part 1 informed Part 2 dosing. In Part 2, patients with chronic hepatitis B on nucleos(t)ide analogue therapy were randomised 11:2 to GSK3389404 (30, 60, 120 mg weekly or 120 mg bi-weekly) or placebo until Day 85. Coprimary endpoints included HBsAg response (≥1.5 logParts 1 and 2 included 12 (9 GSK3389404, 3 placebo) and 66 patients (56 GSK3389404, 10 placebo), respectively. In Part 2, one patient each in the 60 mg weekly, 120 mg weekly and 120 mg bi-weekly arms achieved a HBsAg response. HBsAg reductions were dose-dependent (Day 85: mean 0.34 [60 mg weekly] to 0.75 logGSK3389404 showed an acceptable safety profile and target engagement, with dose-dependent reductions in HBsAg. However, no efficacious dosing regimen was identified.NCT03020745.Hepatitis B virus (HBV) can result in chronic HBV infection, which may ultimately lead to chronic liver disease, primary liver cancer and death; HBV proteins may prevent the immune system from successfully controlling the virus. GSK3389404 is an investigational agent that targets HBV RNA, resulting in reduced viral protein production. This study assessed the safety of GSK3389404 and its ability to reduce the viral proteins in patients with chronic HBV infection. GSK3389404 showed dose-dependent reduction in hepatitis B surface antigen, with an acceptable safety profile. While no clear optimal dose was identified, the findings from this study may help in the development of improved treatment options for patients with chronic HBV infections.

GSK3389404 is a liver‐targeted antisense oligonucleotide that inhibits synthesis of hepatitis B surface antigen and all other hepatitis B virus proteins. This first‐in‐human, randomized, double‐blind, phase 1 study assessed the safety and pharmacokinetics of GSK3389404 administered subcutaneously (SC) in healthy subjects. Four single ascending‐dose cohorts (10 mg, 30 mg, 60 mg, and 120 mg) and 3 multiple ascending‐dose cohorts (30 mg, 60 mg, and 120 mg once weekly for 4 weeks) each comprised 6 subjects randomized to GSK3389404 and 2 subjects randomized to placebo. There were no serious adverse events (AEs) or withdrawals due to AEs. The safety profile did not worsen with repeated dosing. The most frequent treatment‐related AEs were injection site reactions (19.0% [n = 8/42], frequency unrelated to dose levels); all were mild (Grade 1) and resolved without dose modification or discontinuation. GSK3389404 administered subcutaneously was readily absorbed with a time to maximum plasma concentration (Tmax) of 1–4 hours and an elimination half‐life of 3–6 hours in plasma. Plasma area under the concentration‐time curve (AUC) and maximum observed concentration (Cmax) were dose‐proportional. Dose‐normalized plasma AUC from time 0 to infinity averaged 69.9 ng·h/(mL·mg dose) across cohorts, and Cmax 9.5 ng/(mL·mg dose). Pharmacokinetic profiles and parameters were comparable between single and multiple dosing. No accumulation was observed with once‐weekly dosing. The metabolite was undetectable in urine and plasma. In the pooled urine, GSK3389404 was estimated to account for

A tremendous amount has been learned about the Prearchaic (before 9000 BP) Great Basin since we advocated a perspective of sexual division of labor based on Human Behavioral Ecology a decade ago. Many investigators have taken our advice and a few have challenged our assumptions and inferences. One of the most substantive critiques has been that we misunderstood the paleoenvironmental parameters of ungulate populations during the Pleistocene–Holocene Transition (PHT). Simultaneously, behavioral ecologists have advanced our understanding of sexual division of labor among modern foragers, but these studies appear to have gone unnoticed by Great Basin prehistorians. We review findings of the last ten years and suggest that the key to understanding patterning in the PHT still relies on understanding (a) variability in men's and women's foraging goals, (b) the abundance and distribution of large prey, (c) how changing environmental parameters effect both the division of labor and the distribution of resources, and (d) the relative influence of search and handling costs on residence time in PHT wetlands. We suggest that consideration of how paleoenvironmental variability structured sexual division of labor remains key to fully understanding Prearchaic lifeways in the Great Basin.

BACKGROUND: Unemployment among people with schizophrenia remains high despite slight improvements in vocational rehabilitation services and attitudes towards people with mental health disorders over the years. Experts are in a good position to increase our understanding on why this group still experiences such significant barriers to employment. OBJECTIVE: Interviews explored experts’ views on schizophrenia and employment; with a particular focus on individual, attitudinal and structural barriers, as well as available interventions and their outcomes. METHODS:The sample of 20 experts were recruited using theoretical sampling. The experts consisted of: employment specialists, healthcare professionals, activists from patient organisations, academics, caregivers and employers. A thematic approach was used for analysis. RESULTS: Low expectations of healthcare professionals which were often manifested as minimal recognition of employment as an outcome for people with schizophrenia as well as a “benefits trap” were identified as the strongest barriers to employment. In addition, the IPS model was identified as the most effective to support people to work, but lack of funding to implement the model nationally and concerns of poor implementation were raised by the experts. CONCLUSIONS: More research is required to examine which adaptations are needed for vocational interventions in order to implement them successfully.

The prevalent use of ganciclovir and its oral prodrug valganciclovir as prophylaxis and therapy for cytomegalovirus (CMV) infection has increased the awareness of drug resistance, the risk of which increases with prolonged drug exposure, impaired host defenses, or insufficient drug delivery [1]. In high-risk populations such as seronegative recipients of a CMV-seropositive donor organ, the incidence of ganciclovir resistance among treated individuals is estimated to be in the 5%–12% range. Drug resistance is suspected when rising plasma viral loads or progressive disease occur during prolonged antiviral treatment. Although ganciclovir resistance was originally documented by phenotypic testing of CMV culture isolates, this is a slow process, unsuitable in contemporary clinical practice where viral isolation is rarely performed. Instead, genotypic resistance testing is now standard, and is based on the detection of diagnostic mutations in the UL97 kinase gene involved in the initial phosphorylation of ganciclovir or in the UL54 DNA polymerase gene that encodes the antiviral drug target for ganciclovir. The accuracy of genotypic resistance testing depends on a comprehensive and validated database linking specific mutations with levels of drug resistance. Extensive clinical experience has defined a set of UL97 mutations that are the most frequent initial laboratory markers of ganciclovir resistance (M460V/I, H520Q, C592G, A594V, L595S, and C603W), accounting for about 80% of documented cases [1]. In the remaining cases, less common UL97 mutations (clustered at codons 590–607) or UL54 mutation may be the first genetic marker of ganciclovir resistance. UL54 mutations typically add to pre-existing UL97 mutation to increase the level of ganciclovir resistance and confer cross-resistance to other anti-CMV drugs. An ongoing difficulty with interpretation of UL54 mutations is the relatively frequent occurrence of natural sequence polymorphisms unrelated to drug resistance. This difficulty is compounded in prophylaxis studies, where no baseline comparator sequence is available. UL97 and UL54 sequence variants remain incompletely documented despite several surveys of clinical CMV sequences [1–6]. A randomized nonblinded treatment trial comparing 3 weeks of oral valganciclovir and intravenous ganciclovir, followed by 4 weeks of valganciclovir, in solid organ transplant recipients (VICTOR study, NCT00431353) involved 321 subjects [7], of which 275 were included in a published resistance substudy [8]. Study subjects included those with a prior antiviral treatment history. Based on genotypic testing of prospectively collected samples, 13 subjects (4.7% of those tested) were considered to have confirmed or probable ganciclovir resistance mutations during the treatment period (0–49 days). Among the 13 cases, 10 had UL97 mutations only, 1 had both UL97 and UL54 mutations, and 2 were considered to have a probable mixture of resistance-associated and wild-type UL54 sequences without UL97 change [8]. Left unresolved were 110 UL54 amino acid sequence variants that could not be classified as known resistance mutations or natural sequence polymorphism. This study aimed to resolve the status of these sequence variants in relation to ganciclovir resistance. The extensive recombinant phenotyping needed for this purpose relied on recent technical advances in the construction and testing of cloned CMV strains.

Background. In a phase III controlled trial IMproved Protection Against Cytomegalovirus in Transplantation (IMPACT) comparing 200 with 100 days of valganciclovir prophylaxis in 318 cytomegalovirus D+/R— kidney transplant recipients, an equal number of patients (n=3 per arm) had known ganciclovir resistance mutations detected during viral breakthrough. In addition, many other viral sequence variants were observed that were of unknown significance for ganciclovir resistance. Recombinant phenotyping was performed to determine whether the previously uncharacterized genotypic changes affected ganciclovir susceptibility, especially in those receiving the longer duration of prophylaxis. Methods. Sequences encoding individual amino acid substitutions in the UL97 kinase or UL54 DNA polymerase gene were transferred by recombination into a cloned cytomegalovirus laboratory strain, followed by reporter-based yield reduction phenotypic assay of the resulting virus for ganciclovir susceptibility. Results. Twenty-six uncharacterized amino acid substitutions were detected, 2 in UL97 and 24 in UL54. All 10 substitutions in the 200-day arm and 9 of 17 substitutions in the 100-day arm (prioritized based on location and conservation) were selected for phenotyping; one substitution was detected in both subsets. Results were generated for nine of ten 200-day and eight of nine 100-day substitutions, with no substitution demonstrating a significant reduction in ganciclovir susceptibility. The two remaining amino acid substitutions, both in UL54, were not evaluated because of poor viral viability. Conclusion. Phenotypic evaluation of previously uncharacterized viral genotypes in the 200-day valganciclovir prophylaxis group showed no evidence of an increased incidence of genotypic ganciclovir resistance when compared with those in the 100-day prophylaxis group.

Objectives: The identification and in vitro characterization of novel protease mutations strongly associated with known protease resistance mutations. Methods: The association between pairs of protease amino acid substitutions was identified using a database of protease sequences derived from protease inhibitor-experienced patients (n = 803). In vitro characterization included drug susceptibility and viral replication studies performed on recombinant viruses harbouring site-directed mutations. Results: The K55R mutation, which is not a natural polymorphism, was identified to be strongly associated with protease mutations M46I/L and to a lesser extent L24I, I54V and V82A/T/S/F. In vitro characterization of the K55R substitution indicated a primary role for this substitution in increasing replicative capacity in the presence of specific protease mutations. Conclusions: The K55R mutation is a secondary drug resistance mutation that can improve viral replication capacity in the presence of other primary protease mutations.

BACKGROUND & AIMS Setrobuvir is a direct-acting antiviral (DAA) non-nucleoside inhibitor of hepatitis C virus (HCV) polymerase. This study examined interferon-free combinations containing setrobuvir, a ritonavir-boosted protease inhibitor (danoprevir/r) and ribavirin, with/without the nucleoside inhibitor mericitabine in HCV genotype (G)1 patients. METHODS Non-cirrhotic treatment-naive patients (N = 110) were randomized to five groups. Three groups received a 14-day mericitabine/ribavirin lead-in followed by treatment with 3 DAAs (setrobuvir, danoprevir/r, mericitabine) plus ribavirin for 12 weeks (Group A: G1a; D: G1b) or 24 weeks (B: G1a), and two groups received 2 DAAs (setrobuvir, danoprevir/r) plus ribavirin for 12 weeks (E: G1b) or 24 weeks (C: G1a). Efficacy was defined as sustained virological response (HCV RNA

In the SOLO study (APV30002), once-daily antiretroviral treatment with the protease inhibitor fosamprenavir (FPV) 1,400 mg boosted by ritonavir (r) 200 mg plus abacavir/lamivudine (ABC/3TC) was found to be noninferior to nelfinavir plus ABC/3TC over 48 weeks in treatment-naive patients with HIV -1 infection.This interim report presents antiviral efficacy and tolerability data from 211 patients who received FPV/r QD for at least 48 weeks in SOLO and continued this treatment in the follow-on study (APV30005) for up to 120 weeks.APV30005 is an international, multicenter, uncontrolled, open-label, follow-on study conducted to provide continued access to FPV in patients with HIV-1 infection who had participated in previous FPV studies, including SOLO, and to obtain longer-term data on the antiviral response and tolerability of an FPV-containing regimen. Patients who had completed at least 48 weeks of FPV/r therapy in the SOLO study were eligible to enter the follow-on study and continue receiving FPV/r 1,400/200 QD, with study visits every 12 weeks. Their background regimens were chosen at the investigators' discretion and could be changed at any time. Antiviral response end points included plasma HIV-1 RNA levels400 and50 copies/mL, median plasma HIV-1 RNA levels, median and absolute changes from baseline in the CD4 cell count, and the frequency of HIV disease progression. Genotype and phenotype analyses were performed for patients meeting the criterion for virologic failure (defined as plasma HIV -1 RNA1,000 copies/mL on 2 consecutive occasions on or after week 12). Tolerability was assessed in terms of adverse-event reports evaluated by the primary investigator and changes in laboratory values. Assessments were conducted at 12-week intervals during the follow-on study. Data from the baseline visit (day 1 of SOLO) were compared with data from the follow-on study through March 31, 2004, when all patients had completed at least 120 weeks of therapy with FPV/r QD. Because this was a rollover study, no significance testing was performed and all reported results are descriptive.The demographic and baseline characteristics of the patients who received FPV/r QD in this follow on study (N = 211) were similar to those of the 322 patients randomized to receive FPV/r QD in the SOLO study. Their median age was 36 years, 72% were male, 49% were white, and 39% were black. The median baseline plasma HIV 1 RNA level was 4.82 log(10) copies/ mL, and the median baseline CD4+ cell count was 168 cells/mm(3). The median duration of exposure to FPV/r QD from SOLO baseline through the cutoff date was 996 days (142 weeks), ranging from 372 to 1,226 days (53-175 weeks). At week 120, plasma HIV-1 RNA levels400 and50 copies/mL were achieved and maintained in 75% (159) and 66% (139) of patients, respectively, when missing data and discontinuations were counted as failures. The median CD4+ cell count at week 120 was 451 cells/mm(3), a median change from baseline of 292 cells/mm(3). In 14 patients with no baseline resistance who met the criterion for virologic failure, no viral protease resistance mutations were detected. Extended treatment was generally well tolerated. The most frequently reported drug-related grade 2-4 adverse events were diarrhea (22 [10%]), nausea (17 [8%]), drug hypersensitivity (14 [7%], all cases attributed to ABC, which was a study drug in SOLO), and increased triglycerides (14 [7%]). The nature of adverse events reported after 48 weeks of therapy was comparable to that reported before week 48. Adverse events occurred at a similar or lower frequency between weeks 48 and 120 compared with before week 48. Similarly, laboratory abnormalities seen by week 120 were comparable to those seen by week 48, although they were less frequent.Extended treatment (120 weeks) with FPV/r QD in these antiretroviral therapy-naive, HIV-1-infected patients was associated with sustained antiviral response and immunologic improvement. Adverse events had generally developed by 48 weeks of therapy and did not occur at a higher frequency through 120 weeks of treatment.

Objectives: To investigate the emergence of resistance to GW433908 (908), a protease inhibitor (PI) with demonstrated antiviral efficacy, safety and tolerability, when administered once daily (q.d.) with low dose ritonavir (908/r). Design: A 48-week Phase III open-label study (SOLO, APV30002) in which antiretroviral therapy-naive patients (n = 649) were treated with 908/r, (1400 mg/200 mg, q.d.) or nelfinavir [1250 mg, twice daily (b.i.d.)] with two nucleoside reverse transcriptase inhibitors (NRTI), abacavir (300 mg, b.i.d.) and lamivudine (150 mg, b.i.d.). Methods: Viral genotype and phenotype were analysed at baseline and on treatment up to 48 weeks and beyond. Results: Emergence of genotypic resistance was significantly different between the 908/r q.d. and the nelfinavir b.i.d. treatment arms for both PIs (0 versus 50%; P < 0.001) and the NRTI (13% versus 69%; P < 0.001) received. In the nelfinavir arm the key protease mutations D30N and/or L90M were frequently observed. The absence of protease resistance mutations and reduced incidence of NRTI resistance mutations in the 908/r q.d. arm was confirmed by phenotyping, which showed a lack of PI cross-resistance. Conclusions: The absence of resistance to 908 or cross-resistance to other PIs, and reduced NRTI resistance, following a 908/r q.d. regimen supports the use of this boosted PI early in therapy.

One of the major challenges to the successful long-term treatment ofHIV-1 infection is overcoming the development of increasing levelsof antiretroviral resistance that often accompany the failure of suc-cessive treatment regimens. In order to meet this challenge a goodunderstanding of genotypic resistance profiles and the potential forcross-resistance within each class of antiretrovirals is essential. Forthe protease inhibitors (PIs), cross-resistance is complex, as a resultof the large number of mutations involved. Amprenavir and lopinavirare potent PIs used in ritonavir-boosted regimens, often in patientswho have already experienced treatment with other PIs. The resist-ance profiles of these two PIs overlap to a certain extent but also con-tain some important differences that can be exploited in the choice ofoptimal treatment for PI-experienced patients. This article reviewsour own research and that of others, in order to clarify the similaritiesand the differences between the genotypic resistance profiles foramprenavir and lopinavir. Whereas phenotypic data are valuable forunderstanding resistance, HIV-1 genotyping is critical in making theoptimal choice between these two drugs in PI-experienced subjects.

Previous data have indicated that the development of resistance to amprenavir, an inhibitor of the human immunodeficiency virus type 1 protease, is associated with the substitution of valine for isoleucine at residue 50 (I50V) in the viral protease. We present further findings from retrospective genotypic and phenotypic analyses of plasma samples from protease inhibitor-naïve and nucleoside reverse transcriptase inhibitor (NRTI)-experienced patients who experienced virological failure while participating in a clinical trial where they had been randomized to receive either amprenavir or indinavir in combination with NRTIs. Paired baseline and on-therapy isolates from 31 of 48 (65%) amprenavir-treated patients analyzed demonstrated the selection of protease mutations. These mutations fell into four distinct categories, characterized by the presence of either I50V, I54L/I54M, I84V, or V32I+I47V and often included accessory mutations, commonly M46I/L. The I50V and I84V genotypes displayed the greatest reductions in susceptibility to amprenavir, although each of the amprenavir-selected genotypes conferred little or no cross-resistance to other protease inhibitors. There was a significant association, for both amprenavir and indinavir, between preexisting baseline resistance to NRTIs subsequently received during the study and development of protease mutations ( P = 0.014 and P = 0.031, respectively). Our data provide a comprehensive analysis of the mechanisms by which amprenavir resistance develops during clinical use and present evidence that resistance to concomitant agents in the treatment regimen predisposes to the development of mutations associated with protease inhibitor resistance and treatment failure.

Gene–gene interactions may contribute to the genetic variation underlying complex traits but have not always been taken fully into account. Statistical analyses that consider gene–gene interaction may increase the power of detecting associations, especially for low-marginal-effect markers, and may explain in part the “missing heritability.” Detecting pair-wise and higher-order interactions genome-wide requires enormous computational power. Filtering pipelines increase the computational speed by limiting the number of tests performed. We summarize existing filtering approaches to detect epistasis, after distinguishing the purposes that lead us to search for epistasis. Statistical filtering includes quality control on the basis of single marker statistics to avoid the analysis of bad and least informative data, and limits the search space for finding interactions. Biological filtering includes targeting specific pathways, integrating various databases based on known biological and metabolic pathways, gene function ontology and protein–protein interactions. It is increasingly possible to target single-nucleotide polymorphisms that have defined functions on gene expression, though not belonging to protein-coding genes. Filtering can improve the power of an interaction association study, but also increases the chance of missing important findings.

Background The IMPACT study was a randomized, double-blind study comparing 100 to 200 days of VGCV prophylaxis (900 mg once daily) in D+/R− kidney transplant recipients. Although extending the duration of prophylaxis resulted in a significant reduction in confirmed cytomegalovirus (CMV) disease (100-day: 36.8% vs 200-day: 16.1% 1 ), the consequence of extending the duration of prophylaxis on the development of viral resistance remains unknown. Objective To determine whether extending valganciclovir prophylaxis from 100 days to 200 days increased the incidence of ganciclovir resistance. Study design Genotypic analysis of CMV UL97 and UL54 was conducted on virus isolated from patients meeting the predefined resistance analysis criteria (RAC). Results A greater number of patients met the RAC in the 100 day prophylaxis arm (50/163; 31%) compared to the 200 day prophylaxis arm (22/155; 14%). Sequence data were successfully generated for all 200-day patients and 48/50 100-day patients. Three patients in each treatment arm (100 day: 3/163 (1.8%) vs 200 day: 3/155 (1.9%)) had a single known valganciclovir resistance mutation detected (100 day: UL97 gene: M460V, C592G twice; 200 day: UL97 gene: C603W, M460V and UL54 gene: P522S). Overall, a resistance mutation was more likely to be detected if the patient met the RAC during prophylaxis (5/12 (42%)) compared to post-prophylaxis (1/58 (2%)). All six patients with known ganciclovir resistance mutations cleared the virus; three cleared virus without treatment and three cleared virus following treatment. Conclusions Extending valganciclovir prophylaxis from 100 days to 200 days did not significantly affect the incidence of ganciclovir resistance.

The HIV-1 genome encodes an essential protease enzyme which is one of the major targets of antiviral therapy (1–3). Protease inhibitors (PIs) have been proven to be potent antiviral agents and their introduction in 1995 led to the era of highly active antiretroviral therapy, the most potent and prescribed treatment of HIV infections today (4, 5). Although resistance to HIV-1 reverse transcriptase inhibitors had been described in the late 1980s (6), it was originally thought that PIs would be much less prone to drug evasion because of intrinsic genetic and structural constraints. Contrary to these expectations however, a substantial number of patients in the initial studies with PIs experienced drug failure due to the accumulation of multiple mutations in the HIV-1 protease gene (7–15). To understand the mechanisms leading to PI resistance better, it is important to fi rst briefl y review the general structure of the enzyme as well as the interactions involved in inhibitor binding.

The human immunodefi ciency virus (HIV) is a member of the Retroviridae family (lentivirus genus), characterized by the presence of a virally encoded reverse transcriptase (RT) enzyme (1). Upon cell entry, the RT enzyme is responsible for the conversion of the single-stranded viral genomic RNA into a complementary double-stranded DNA copy (cDNA). The RT enzyme possesses both RNA-dependent and DNAdependent DNA polymerase activities as well as RNase H activity, which is responsible for the degradation of the genomic RNA and tRNA primer (2, 3). The process of cDNA synthesis involves a complex of the RT enzyme, the template (either genomic RNA or single-stranded DNA), the tRNA primer and deoxynucleotides (dNTPs). Crystal structures of HIV-1 RT either unliganded (4–6) or in complex with double-stranded DNA (7–10) have allowed for the three-dimensional description of the enzyme. RT is a heterodimer composed of the p66 and p51 subunits. The p51 subunit is generated through proteolytic cleavage of p66 by HIV protease and is composed of the fi rst 440 residues of p66 (the remaining 120 residues of p66 forming the C-terminal RNase H domain of the enzyme). The dimerization interface between the subunits is quite extensive, involving several conserved areas (11). On the basis of the resemblance of the p66 subunit to a right hand, common regions within p66 and p51 have been identifi ed and termed as the ‘fi ngers’, ‘palm’, ‘thumb’, and ‘connection’ subdomains. The folding of the individual subdomains is similar in p66 and p51, but their spatial arrangement differs signifi cantly (Fig. 1). The p66 subunit has an open quaternary structure and contains the active sites for both the polymerase and RNase H activities while p51 adopts a more closed conformation and mainly plays a structural role inducing p66 to perform catalysis. RT is highly fl exible and undergoes conformational changes during the course of the enzymatic process. In the absence of primer-template substrate, the p66 ‘thumb’ domain is folded down and closes the DNA-binding cleft. Upon primer-template binding, the ‘thumb’ folds back in an upright position, opening up an area delineated by amino acids from the p66 ‘fi ngers’, ‘palm’ and ‘thumb’ subdomains that precisely place the substrate for catalysis. These regions of p66 responsible for the correct placement of the substrate are commonly referred to as the ‘primer’ and ‘template’ grips. In this arrangement, the primer 3′-OH terminus lies near the three catalytic residues (D110, D185, D186) of the polymerase-active site, and is poised for attack on the incoming nucleotide while the rest of the duplex extends on the surface toward the RNase H domain.

Objective: To identify optimal first-line therapies based on the rate of virologic success (VS) and the preservation of future treatment options in antiretroviral therapy (ART)-naive subjects. Design: Systematic overview of genotypic resistance mutations from clinical trials of combination ART. Methods: Various sources were searched for studies in ART-naive subjects providing virologic response rates and genotypes from subjects with virologic failure. The International AIDS Society-USA genotypic resistance guidelines were used to calculate regimen resistance cost (RC reg ) and number of active drug (AD) scores for each regimen and to rank the regimens. Results: Intra- and interstudy comparisons showed higher VS rates for nonnucleoside reverse transcriptase inhibitor (NNRTI) regimens (range: 51%-76%) and boosted protease inhibitor (boosted PI) regimens (range: 55%-79%). Boosted PI failures had the lowest RC reg (range: 0.12-0.21) and the highest AD (range: 19.80-20.18) scores. NNRTI failures had higher RC reg (range: 0.00-1.22) and lower AD (range: 16.83-21) scores. Conclusions: NNRTI and boosted PI regimens provide the highest rates of VS in treatment-naive HIV-infected persons. Treatment option scores were higher in subjects who failed boosted PI-containing regimens versus NNRTI-containing regimens, however.

Development of in vitro resistance to GW640385, a new human immunodeficiency virus type 1 protease inhibitor, was studied. Variants characterized included one with 50-fold resistance and amino acid substitutions L10F/G16E/E21K/A28S/M46I/F53L/A71V (protease) and L449F/P453T (Gag). The A28S substitution substantially reduced replication capacity.

The archaeological record of the Pleistocene/Holocene transition (PHT) demonstrates that the technology and mobility of Prearchaic hunter-gatherers differed dramatically from later Holocene foragers, suggesting a hunting-oriented subsistence. However, meager PHT faunal assemblages imply a generalized, broad-spectrum diet. Ethnographic analogy fails to provide a behavioral framework for understanding this discrepancy because the resource structure of the PHT differed utterly from the ethnographic present. Palaeoenvironmental data alone are incapable of retrodicting ancient diets without an understanding of foraging costs in extinct resource landscapes. This paper reviews recent studies using behavioral ecology as a theoretical framework for simulating foraging behavior in a PHT resource landscape. The simulation for Railroad Valley, Nevada, suggests the explanation for the diversity of subsistence remains in PHT records lies in different foraging strategies for men and women, rather than risk aversion alon...

The intra-grating temperature profile of a chirped fiber Bragg grating was determined using integration of the changes in power reflectance spectra whilst it was subjected to a nonuniform temperature distribution.