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Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient's disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase's ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: CS acknowledges grant support from AstraZeneca, Boehringer-Ingelheim, BMS, Pfizer, Roche-Ventana, Invitae (previously Archer Dx, collaboration in minimal residual disease sequencing technologies), Ono Pharmaceutical, and Personalis; is an AstraZeneca advisory board member and chief investigator for the AZ MeRmaiD 1 and 2 clinical trials and is also co-chief investigator of the NHS Galleri trial funded by GRAIL and a paid member of GRAIL’s scientific advisory board; receives consultant fees from Achilles Therapeutics (also a scientific advisory board member), Bicycle Therapeutics (also a scientific advisory board member), Genentech, Medicxi, China Innovation Centre of Roche (CICoR) formerly Roche Innovation Centre – Shanghai, Metabomed (until July 2022) and the Sarah Cannon Research Institute; has received honoraria from Amgen, AstraZeneca, Pfizer, Novartis, GlaxoSmithKline, MSD, Bristol Myers Squibb, Illumina, and Roche-Ventana; had stock options in Apogen Biotechnologies and GRAIL until June 2021, and currently has stock options in Epic Bioscience, Bicycle Therapeutics, and has stock options and is co-founder of Achilles Therapeutics; is listed as an inventor on a European patent application relating to assay technology to detect tumour recurrence (PCT/GB2017/053289), the patent has been licensed to commercial entities and, under his terms of employment, CS is due a revenue share of any revenue generated from such license(s); holds patents relating to targeting neoantigens (PCT/EP2016/059401), identifying patient response to immune checkpoint blockade (PCT/EP2016/071471), determining HLA LOH (PCT/GB2018/052004), predicting survival rates of patients with cancer (PCT/GB2020/050221), identifying patients who respond to cancer treatment (PCT/GB2018/051912), a US patent relating to detecting tumour mutations (PCT/US2017/28013), methods for lung cancer detection (US20190106751A1) and both a European and US patent related to identifying insertion/deletion mutation targets (PCT/GB2018/051892) and is listed as a co-inventor on a patent application to determine methods and systems for tumour monitoring (PCT/EP2022/077987) and is a named inventor on a provisional patent protection related to a ctDNA detection algorithm. NM has received consultancy fees and has stock options in Achilles Therapeutics. NM holds European patents relating to targeting neoantigens (PCT/EP2016/ 059401), identifying patient response to immune checkpoint blockade (PCT/ EP2016/071471), determining HLA LOH (PCT/GB2018/052004), predicting survival rates of patients with cancer (PCT/GB2020/050221). All other authors declare no competing interests., (Copyright: © 2023 Watkins et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

We have previously shown that the transcription factor HNF4A is required for the formation of hepatic progenitor cells from endoderm that has been derived from human induced pluripotent stem cells (iPSCs). We reasoned that we could uncover regulatory pathways with new roles in hepatocyte differentiation by identifying cellular processes that regulate HNF4A. We therefore performed a screen of 1120 small molecules with well-characterized mechanisms of action to detect those that affect the abundance of HNF4A in iPSC-derived hepatic progenitor cells. This approach uncovered several small molecules that depleted HNF4A. Of those, we chose to focus on an inhibitor of heat shock protein 90 beta (HSP90β). We show that mutation of the gene encoding HSP90β represses hepatocyte differentiation during the formation of hepatocytes from iPSCs. We reveal that HSP90β, although dispensable for expression of HNF4A mRNA, directly interacts with HNF4A protein to regulate its half-life. Our results demonstrate that HSP90β has an unappreciated role in controlling hepatic progenitor cell formation and highlight the efficiency of using small-molecule screens during the differentiation of iPSCs to reveal new molecular mechanisms that control hepatocyte formation., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2017. Published by The Company of Biologists Ltd.)

Background: Sufficient evidence suggests that preoperative biliary stenting is associated with increased complication rates after pancreaticoduodenectomy., Methods: Surveillance, Epidemiology, and End Results (SEER) and linked Medicare claims data (1992-2007) were used to identify patients with pancreatic cancer who underwent pancreaticoduodenectomy. We evaluated trends in the use of preoperative biliary stenting, timing of physician visits relative to stenting, and time to surgical resection and symptoms in stented and unstented patients., Results: Pancreaticoduodenectomy was performed in 2,573 patients, and 52.6% of patients underwent preoperative biliary stenting (N = 1,354). Of these, 75.3% underwent endoscopic stenting only, 18.9% received a percutaneous stent, and 5.8% underwent both procedures. The overall stenting rate increased from 29.6% of patients between 1992 and 1995 to 59.1% between 2004 and 2007 (P < .0001). Preoperative stenting was more common in patients with jaundice, cholangitis, pruritus, or coagulopathy (P < .05 for all). Of stented patients, 77.7% had had a stent placed prior to seeing a surgeon. Stenting prior to surgical consultation was associated with longer indwelling stent time compared to stenting after surgical consultation (37.3 vs 27.0 days, P < .0001). In addition, stented patients had longer times from surgeon visit to pancreatectomy than those who had not received stents (24.2 days vs 17.2 days, P < .0001)., Conclusion: Use of preoperative biliary stenting doubled between 1992 and 2007 despite evidence that stenting is associated with increased perioperative infectious complications. The majority of stenting occurred prior to surgical consultation and is associated with significant delay in time to operation. Surgeons should be involved early in order to prevent unnecessary stenting and improve outcomes., (Copyright © 2013 Mosby, Inc. All rights reserved.)

Background: Current guidelines recommend minimally invasive breast biopsy (MIBB) as the gold standard for the diagnosis of breast lesions. The purpose of this study was to describe geographic patterns and time trends in the use of MIBB in Texas., Methods: We used 100% Texas Medicare claims data (2000-2008) to identify women older than 66 years of age who underwent breast biopsy. Biopsies were classified as open or MIBB. Time trends, racial/ethnic variation, and geographic variation in the use of biopsy techniques were examined., Results: A total of 87,165 breast biopsies were performed on 75,518 breast masses in 67,582 women; 65.8% of the initial biopsies were MIBB. Radiologists performed 70.3% and surgeons performed 26.2% of MIBB. Surgeons performed 94.2% of open biopsies. Hispanic women were less likely to undergo MIBB (55.9%) compared with white (66.6%) and black (68.9%) women (p < 0.0001). Women undergoing MIBB were also more likely to live in metropolitan areas and have higher income and educational levels (p < 0.0001). The rate of MIBB increased from 44.4% in 2001 to 79.1% in 2008 (p < 0.0001). There are clear geographic patterns in MIBB use, with highest use near major cities. Although rates are increasing overall, rates of improvement in the use of MIBB vary considerably across geographic regions and remain persistently low in more rural areas., Conclusions: Despite an increase in the use of MIBB over time, MIBB use was consistently lower than recommended. We must identify specific barriers in rural areas to effectively change practice and achieve the statewide goal of 90% MIBB., (Copyright © 2013 American College of Surgeons. Published by Elsevier Inc. All rights reserved.)

Background: Gallbladder disease is common and, if managed incorrectly, can lead to high rates of morbidity, mortality, and extraneous costs. The most common complications of gallstones include biliary colic, acute cholecystitis, common bile duct stones, and gallstone pancreatitis. Ultrasound is the initial imaging modality of choice. Additional diagnostic and therapeutic studies including computed tomography, magnetic resonance imaging, magnetic resonance cholangiopancreatography, endoscopic ultrasound, and endoscopic retrograde cholangiopancreatography are not routinely required but may play a role in specific situations., Discussion: Biliary colic and acute cholecystitis are best treated with early laparoscopic cholecystectomy. Patients with common bile duct stones should be managed with cholecystectomy, either after or concurrent with endoscopic or surgical relief of obstruction and clearance of stones from the bile duct. Mild gallstone pancreatitis should be treated with cholecystectomy during the initial hospitalization to prevent recurrence. Emerging techniques for cholecystectomy include single-incision laparoscopic surgery and natural orifice transluminal endoscopic surgery. Early results in highly selected patients demonstrate the safety of these techniques. The management of complications of the gallbladder should be timely and evidence-based, and choice of procedures, particularly for common bile duct stones, is largely influenced by facility and surgeon factors.

Background: Routine preoperative laboratory testing for ambulatory surgery is not recommended., Methods: Patients who underwent elective hernia repair (N = 73,596) were identified from the National Surgical Quality Improvement Program (NSQIP) database (2005-2010). Patterns of preoperative testing were examined. Multivariate analyses were used to identify factors associated with testing and postoperative complications., Results: A total of 46,977 (63.8%) patients underwent testing, with at least one abnormal test recorded in 61.6% of patients. In patients with no NSQIP comorbidities (N = 25,149) and no clear indication for testing, 54% received at least one test. In addition, 15.3% of tested patients underwent laboratory testing the day of the operation. In this group, surgery was done despite abnormal results in 61.6% of same day tests. In multivariate analyses, testing was associated with older age, ASA (American Society of Anesthesiologists) class >1, hypertension, ascites, bleeding disorders, systemic steroids, and laparoscopic procedures. Major complications (reintubation, pulmonary embolus, stroke, renal failure, coma, cardiac arrest, myocardial infarction, septic shock, bleeding, or death) occurred in 0.3% of patients. After adjusting for patient and procedure characteristics, neither testing nor abnormal results were associated with postoperative complications., Conclusions: Preoperative testing is overused in patients undergoing low-risk, ambulatory surgery. Neither testing nor abnormal results were associated with postoperative outcomes. On the basis of high rates of testing in healthy patients, physician and/or facility preference and not only patient condition currently dictate use. Involvement from surgical societies is necessary to establish guidelines for preoperative testing.

After initiation of antiretroviral therapy (ART), HIV loads and frequencies of HIV epitope-specific immune responses decrease. A diverse virus-specific T cell receptor (TCR) repertoire allows the host to respond to viral epitope diversity, but the effect of antigen reduction as a result of ART on the TCR repertoire of epitope-specific CD8(+) T cell populations has not been well defined. We determined the TCR repertoires of 14 HIV-specific CD8(+) T cell responses from 8 HIV-positive individuals before and after initiation of ART. We used multiparameter flow cytometry to measure the distribution of memory T cell subsets and the surface expression of PD-1 on T cell populations and T cell clonotypes within epitope-specific responses from these individuals. Post-ART, we noted decreases in the frequency of circulating epitope-specific T cells (P = 0.02), decreases in the number of T-cell clonotypes found within epitope-specific T cell receptor repertoires (P = 0.024), and an overall reduction in the amino acid diversity within these responses (P < 0.0001). Despite this narrowing of the T cell response to HIV, the overall hierarchy of dominant T cell receptor clonotypes remained stable compared to that pre-ART. CD8(+) T cells underwent redistributions in memory phenotypes and a reduction in CD38 and PD-1 expression post-ART. Despite extensive remodeling at the structural and phenotypic levels, PD-1 was expressed at higher levels on dominant clonotypes within epitope-specific responses before and after initiation of ART. These data suggest that the antigen burden may maintain TCR diversity and that dominant clonotypes are sensitive to antigen even after dramatic reductions after initiation of ART.

Flexibility of the HIV-specific T-cell receptor repertoire is a hallmark of HIV-1 infection. Altered differentiation of HIV-specific CD45RO(+)/CCR7(-) (TemRO) CD8(+) effector-memory T cells into CD45RA(+)/CCR7(-) (TemRA) CD8(+) effector-memory T cells as well as increased expression of the senescence marker CD57 has been frequently observed HIV-1 infection, but the structural relationship between clonal expansion and T-cell differentiation has not been defined. In this study, we demonstrate that HIV-specific clonotypes have differing degrees of TemRA differentiation but always maintain a significant proportion of TemRO-phenotype cells. These data indicate that structural constraints of the TCR/peptide major histocompatibility complex interaction play a central role in the TemRA differentiation of HIV-specific CD8(+) T cells in chronic HIV-1 infection. Clonotypes with a predominantly TemRA phenotype had a substantial fraction of cells without expression of CD57; and in contrast to the high clonotypic variability of TemRA differentiation, expression of CD57 was highly correlated among T-cell clonotypes within epitope-specific responses, indicating TCR-independent expression of CD57 in vivo. Our data highlight the importance of the structural composition of the TCR repertoire for the effector-memory differentiation of the immune response in chronic viral infections and suggest that TCR-dependent and -independent homeostasis shapes the pathogen-specific effector-memory repertoire in vivo.

Risk factors associated with respiratory failure during respiratory syncytial virus (RSV) infection have not been assessed in adults. We identified RSV by quantitative reverse transcription polymerase chain reaction in 58 adults during the 2007-2008 winter. Clinical variables and respiratory secretion viral loads were compared in 26 outpatients and 32 inpatients. Cardiopulmonary diseases were more common among inpatients than outpatients (91% vs 31%, P = .0001), whereas mean RSV load was similar. Nasal viral load was higher in ventilated vs nonventilated hospitalized patients (log(10) 3.7 +/- 1.7 plaque-forming units (PFUs)/mL vs 2.4 +/- 1.1 PFUs/mL, P = .02), and high viral load was independently associated with respiratory failure.

T-cell receptor (TCR) diversity of virus-specific CD8+ T cells likely helps prevent escape mutations in chronic viral infections. To understand the dynamics of the virus-specific T cells in more detail, we followed the evolution of the TCR repertoire specific for a dominant HLA-B*08-restricted epitope in Nef (FLKEKGGL) in a cohort of subjects infected with HIV. Epitope-specific CD8+ T cells used structurally diverse TCR repertoires, with different TCRbeta variable regions and with high amino acid diversity within antigen recognition sites. In a longitudinal study, distinct Vbeta populations within the HIV-specific TCR repertoire expanded simultaneously with changes in plasma viremia, whereas other Vbeta populations remained stable or even decreased. Despite antigenic variation in some subjects, all subjects had the consensus sequence present during the study period. Functional analysis of distinct Vbeta populations revealed differences in HIV-specific IFN-gamma secretion ex vivo as well as differences in tetramer binding, indicating functional heterogeneity among these populations. This contrasts with findings in a subject on antiretroviral therapy with suppression of viremia to less than 50 copies/mL, where we observed long-term persistence of a single clonotype. Our findings illustrate the flexibility of a heterogeneous HIV-1-specific CD8+ TCR repertoire in subjects with partial control of viremia.