Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment and propagation, affecting the accuracy of PDX modeling of human cancer. Here, we exhaustively analyze copy number alterations (CNAs) in 1,451 PDX and matched patient tumor (PT) samples from 509 PDX models. CNA inferences based on DNA sequencing and microarray data displayed substantially higher resolution and dynamic range than gene expression-based inferences, and they also showed strong CNA conservation from PTs through late-passage PDXs. CNA recurrence analysis of 130 colorectal and breast PT/PDX-early/PDX-late trios confirmed high-resolution CNA retention. We observed no significant enrichment of cancer-related genes in PDX-specific CNAs across models. Moreover, CNA differences between patient and PDX tumors were comparable to variations in multiregion samples within patients. Our study demonstrates the lack of systematic copy number evolution driven by the PDX mouse host.

Oxidative Stress and Cardiovascular Risk in Type 1 Diabetes Mellitus: Insights From the DCCT/EDIC Study

Background

Hyperglycemia leading to increased oxidative stress is implicated in the increased risk for the development of macrovascular and microvascular complications in patients with type 1 diabetes mellitus.

Methods and Results

A random subcohort of 349 participants was selected from the DCCT / EDIC (Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications) cohort. This included 320 controls and 29 cardiovascular disease cases that were augmented with 98 additional known cases to yield a case cohort of 447 participants (320 controls, 127 cases). Biosamples from DCCT baseline, year 1, and closeout of DCCT , and 1 to 2 years post‐ DCCT ( EDIC years 1 and 2) were measured for markers of oxidative stress, including plasma myeloperoxidase, paraoxonase activity, urinary F 2α isoprostanes, and its metabolite, 2,3 dinor‐8 iso prostaglandin F 2α . Following adjustment for glycated hemoblobin and weighting the observations inversely proportional to the sampling selection probabilities, higher paraoxonase activity, reflective of antioxidant activity, and 2,3 dinor‐8 iso prostaglandin F 2α , an oxidative marker, were significantly associated with lower risk of cardiovascular disease (−4.5% risk for 10% higher paraoxonase, P <0.003; −5.3% risk for 10% higher 2,3 dinor‐8 iso prostaglandin F 2α , P =0.0092). In contrast, the oxidative markers myeloperoxidase and F 2α isoprostanes were not significantly associated with cardiovascular disease after adjustment for glycated hemoblobin. There were no significant differences between DCCT intensive and conventional treatment groups in the change in all biomarkers across time segments.

Conclusions

Heightened antioxidant activity (rather than diminished oxidative stress markers) is associated with lower cardiovascular disease risk in type 1 diabetes mellitus, but these biomarkers did not change over time with intensification of glycemic control.

Clinical Trial Registration

URL : https://www.clinicaltrials.gov . Unique identifiers: NCT 00360815 and NCT 00360893.

Web-Based Stress Management for Newly Diagnosed Patients With Cancer (STREAM): A Randomized, Wait-List Controlled Intervention Study

Purpose

Being diagnosed with cancer causes major psychological distress; however, a majority of patients lack psychological support during this critical period. Internet interventions help patients overcome many barriers to seeking face-to-face support and may thus close this gap. We assessed feasibility and efficacy of Web-based stress management (STREAM [Stress-Aktiv-Mindern]) for newly diagnosed patients with cancer.

Patients and Methods

In a randomized controlled trial, patients with cancer who had started first-line treatment within the previous 12 weeks were randomly assigned to a therapist-guided Web-based intervention or a wait-list (control), stratified according to distress level (≥ 5 v < 5 on scale of 0 to 10). Primary efficacy end point was quality of life after the intervention (Functional Assessment of Chronic Illness Therapy–Fatigue). Secondary end points included distress (Distress Thermometer) and anxiety or depression (Hospital Anxiety and Depression Scale). Treatment effect was assessed with analyses of covariance, adjusted for baseline distress.

Results

A total of 222 of 229 screened patients applied online for participation. Between September 2014 and November 2016, 129 newly diagnosed patients with cancer, including 92 women treated for breast cancer, were randomly assigned to the intervention (n = 65) or control (n = 64) group. Adherence was good, with 80.0% of patients using ≥ six of eight modules. Psychologists spent 13.3 minutes per week (interquartile range, 9.5-17.9 minutes per week) per patient for online guidance. After the intervention, quality of life was significantly higher (Functional Assessment of Chronic Illness Therapy–Fatigue: mean, 8.59 points; 95% CI, 2.45 to 14.73 points; P = .007) and distress significantly lower (Distress Thermometer: mean, −0.85; 95% CI, −1.60 to −0.10; P = .03) in the intervention group as compared with the control. Changes in anxiety or depression were not significant in the intention-to-treat population (Hospital Anxiety and Depression Scale: mean, −1.28; 95% CI, −3.02 to 0.45; P = .15). Quality of life increased in the control group with the delayed intervention.

Conclusion

The Web-based stress management program STREAM is feasible and effective in improving quality of life.

Efficacy of an internet-based cognitive behavioral stress management training in women with idiopathic preterm labor: A randomized controlled intervention study

OBJECTIVE

This randomized controlled trial aimed at evaluating the efficacy of an internet-based cognitive behavioral stress management program (IB-CBSM) for pregnant women with preterm labor (PTL) on birth outcome and stress-related psychological and biological parameters.

METHODS

93 pregnant women with PTL (gestational age 18-32) were assigned to either the IB-CBSM (n=50) or a control group (CG) based on distraction (n=43). Participants in both groups worked through six weekly modules. Birth outcome measures included gestational age, neonatal weight and length at birth and the rate of preterm birth (PTB). Questionnaires assessed psychological wellbeing and the activity of the HPA-axis was measured with the cortisol awakening reaction (CAR), both before (T1) and after the intervention (T2).

RESULTS

Birth outcome and psychological wellbeing did not differ between IB-CBSM and CG. However, psychological wellbeing was higher after both interventions (PSS: η_p²=0.455, STAIX1: η_p²=0.455, STAIX2: η_p²=0.936, PRAT: η_p²=0.465, EPDS: η_p²=0.856). Cortisol levels were stable and did not alter differently between groups from T1 to T2. Higher cortisol levels were associated with lower gestational age at birth, whereas no significant correlations were found between weight and length at birth.

CONCLUSIONS

Although there were no significant differences between the two groups and birth outcome, psychological and biological parameters, both interventions (CBSM and CG) showed equivalent effects and proved to be beneficial with regard to psychosocial distress and well-being. Further research is needed to investigate CBSM and distraction interventions for pregnant women at risk for PTB together with a non-intervention control condition.

Web-based stress management for newly diagnosed cancer patients (STREAM): A randomized, wait-list controlled intervention study

LBA10002

Background: Being diagnosed with cancer causes major distress, yet the majority of newly diagnosed cancer patients (pts) lack psychological support. Internet interventions overcome many barriers for seeking support. We assess efficacy and feasibility of a web-based minimal-contact stress management intervention (STREAM) for newly diagnosed cancer pts. Methods: In a prospective, wait-list controlled trial, newly diagnosed cancer pts were randomized within 12 weeks of starting anti-cancer treatment to an immediate or delayed (control group) 8-week, web-based intervention. The intervention consisted of 8 modules with weekly written feedback by a psychologist (“minimal-contact”) based on well-established stress management manuals. The aim of this study was to evaluate efficacy in terms of improvement in QoL (FACIT-F), decrease in distress (DT), anxiety/depression (HADS), as compared to pts in the wait-list group. 120 pts were needed to show (80% power, 2-sided α of 0.05) a clinically meaningful difference of ≥ 9 in FACT score after the immediate intervention (week 8 = T2). Results: 225 pts applied online. 128 pts were randomized. Median age was 52 (22-77)y. 108 (84%) were female. The majority of pts were treated in the curative setting (117pts; 91%), with chemotherapy (74 pts; 58%), for breast cancer (91pts; 71%). Self-reported distress at baseline ( = stratification factor) was above 4 on a 10-point scale (DT) with 96 pts (75%). At T2, QoL (FACIT-F) was sign. increased (p = 0.044; ANCOVA adjusted for baseline-distress) and distress sign. lowered (p = 0.032) in the intervention group as compared to the wait-list control. Median score (lower/upper quartile) for FACIT-F at baseline/T2 was 101.0(80.8/120)/119.0(98.0/132) and 108.3(87.8/124.0) /109.5(97.2/121.0); of DT at baseline/T2 was 6(5/8)/4(3/6) and 6(5/8)/6(4/7) for the intervention and control group, respectively. Decrease in HADS was not sign. different between the groups (p = 0.273). Conclusions: With STREAM, we open the field of minimal-contact online interventions to newly diagnosed cancer pts and show that an 8-week web-based stress management program is feasible and effective in improving QoL and distress. Clinical trial information: NCT02289014.

Web-based stress management for newly diagnosed cancer patients (STREAM): A randomized, wait-list controlled intervention study

LBA10002

The full, final text of this abstract will be available at abstracts.asco.org at 2:00 PM (EDT) on Friday, June 2, 2017, and in the Annual Meeting Proceedings online supplement to the June 20, 2017, issue of the Journal of Clinical Oncology. Onsite at the Meeting, this abstract will be printed in the Saturday edition of ASCO Daily News.

Intranasal oxytocin increases facial expressivity, but not ratings of trustworthiness, in patients with schizophrenia and healthy controls

BACKGROUND

Blunted facial affect is a common negative symptom of schizophrenia. Additionally, assessing the trustworthiness of faces is a social cognitive ability that is impaired in schizophrenia. Currently available pharmacological agents are ineffective at improving either of these symptoms, despite their clinical significance. The hypothalamic neuropeptide oxytocin has multiple prosocial effects when administered intranasally to healthy individuals and shows promise in decreasing negative symptoms and enhancing social cognition in schizophrenia. Although two small studies have investigated oxytocin's effects on ratings of facial trustworthiness in schizophrenia, its effects on facial expressivity have not been investigated in any population.

METHOD

We investigated the effects of oxytocin on facial emotional expressivity while participants performed a facial trustworthiness rating task in 33 individuals with schizophrenia and 35 age-matched healthy controls using a double-blind, placebo-controlled, cross-over design. Participants rated the trustworthiness of presented faces interspersed with emotionally evocative photographs while being video-recorded. Participants' facial expressivity in these videos was quantified by blind raters using a well-validated manualized approach (i.e. the Facial Expression Coding System; FACES).

RESULTS

While oxytocin administration did not affect ratings of facial trustworthiness, it significantly increased facial expressivity in individuals with schizophrenia (Z = -2.33, p = 0.02) and at trend level in healthy controls (Z = -1.87, p = 0.06).

CONCLUSIONS

These results demonstrate that oxytocin administration can increase facial expressivity in response to emotional stimuli and suggest that oxytocin may have the potential to serve as a treatment for blunted facial affect in schizophrenia.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

Patient satisfaction and psychological well-being after internet-based cognitive behavioral stress management (IB-CBSM) for women with preterm labor: A randomized controlled trial

OBJECTIVE AND METHODS

Despite its value for the management of psychological burden, little is known about the efficacy of and patient satisfaction with internet-based cognitive behavioral stress management (IB-CBSM) for women with preterm labor. The present study sets out to analyze stress/anxiety reduction, patient satisfaction and patient's working alliance in a group of 58 women with preterm labor participating in an online psychological stress management project. As part of the project, women were randomly assigned to online stress management or a control condition.

RESULTS

Levels of stress and anxiety decreased significantly in both conditions from pre- to post-treatment measure. Participants in IB-CBSM reported significant higher working alliance inventory (WAI) scores in the task and goal subscale (p<.001; p<.05) than women in the control condition. In Addition the IB-CBSM group showed significant correlations of the WAI subscale task and goal and the stress/anxiety outcome. Regarding patient satisfaction, women in the IB-CBSM reported significantly higher satisfaction scores (p<.001) than women in the control condition. WAI explained nearly 40% of the variance in patient satisfaction. Furthermore, WAI mediates, at least in part, the relationship between group condition and patient satisfaction.

CONCLUSION

The current analysis indicated that participants in IB-CBSM had higher WAI scores and were more satisfied with the program. In addition only the IB-CBSM group showed significant correlations of the WAI with the stress/anxiety reduction outcome. Based on these findings, it can be presumed that measures of agreement with working alliance parameters, especially task and goal components, are substantially important for more effective and satisfactory therapeutic interventions.

Internet-based stress management for women with preterm labour--a case-based experience report

Pregnant women with preterm labour (PTL) in pregnancy often experience increased distress and anxieties regarding both the pregnancy and the child's health. The pathogenesis of PTL is, among other causes, related to the stress-associated activation of the maternal-foetal stress system. In spite of these psychobiological associations, only a few research studies have investigated the potential of psychological stress-reducing interventions. The following paper will present an online anxiety and stress management self-help program for pregnant women with PTL. Structure and content of the program will be illustrated by a case-based experience report. L.B., 32 years (G3, P1), was recruited at gestational week 27 while hospitalized for PTL for 3 weeks. She worked independently through the program for 6 weeks and had regular written contact with a therapist. Processing the program had a positive impact on L.B.'s anxiety and stress levels, as well as on her experienced depressive symptoms and bonding to the foetus. As PTL and the risk of PTB are associated with distress, psychological stress-reducing interventions might be beneficial. This study examines the applicability of an online intervention for pregnant women with PTL. The case report illustrates how adequate low-threshold psychological support could be provided to these women.

Accurate test of chiral dynamics in the γp→π0p reaction

A precision measurement of the differential cross sections dσ/dΩ and the linearly polarized photon asymmetry Σ≡(dσ⊥-dσ∥)/(dσ⊥+dσ∥) for the γp→π0p reaction in the near-threshold region has been performed with a tagged photon beam and almost 4π detector at the Mainz Microtron. The Glasgow-Mainz photon tagging facility along with the Crystal Ball/TAPS multiphoton detector system and a cryogenic liquid hydrogen target were used. These data allowed for a precise determination of the energy dependence of the real parts of the S- and all three P-wave amplitudes for the first time and provide the most stringent test to date of the predictions of chiral perturbation theory and its energy region of agreement with experiment.

Influence of test technique on sensitization status of patients on the kidney transplant waiting list

The exquisitely sensitive single antigen bead (SAB) technique was shown to detect human leukocyte antigen (HLA) antibodies in sera of healthy male blood donors. Such false reactions can have an impact on critical decisions, especially with respect to the determination of unacceptable HLA-antigen mismatches in patients awaiting a kidney transplant. We tested pretransplant sera of 534 patients on the kidney waiting list using complement-dependent cytotoxicity (CDC), enzyme-linked immunosorbent assay (ELISA) and SAB in parallel. Evidence of HLA antibodies was obtained in 5% of patients using CDC, 14% using ELISA, and 81% using SAB. Among patients without history of an immunizing event, 77% showed evidence of HLA antibodies in SAB. In contrast 98% of these patients were negative in ELISA and CDC. In patients without an immunizing event, SAB-detected antibodies reacted not always weakly but with mean fluorescence intensity (MFI) values as high as 14 440. High-MFI-value antibodies were found in some of these patients with HLA specificities that are rather common in general population, consideration of which would lead to unjustified exclusion of potential kidney donors. False SAB reactions can be unveiled by testing with additional antibody assays. Denial of donor kidneys to recipients based on HLA-antibody specificities detected exclusively in the SAB assay is not advisable.

No impact of KIR-ligand mismatch on allograft outcome in HLA-compatible kidney transplantation

Natural killer (NK) cell function can be modulated by the killer cell immunoglobulin-like receptors (KIR) which interact with human leukocyte antigen (HLA) class I molecules on target cells. KIR-ligand mismatching has recently been shown by van Bergen et al. (American Journal of Transplantation 2011; 11(9): 1959-1964) to be a significant risk factor for long-term graft loss in HLA-A, -B and -DR compatible kidney transplants. To verify this potentially important finding, we performed genotyping of 608 deceased-donor kidney graft recipients and their HLA-A, -B and -DR compatible donors for KIR and HLA, using samples and clinical data provided by the Collaborative Transplant Study. Graft survival of KIR-ligand-matched and -mismatched transplants was compared. We found no impact of KIR-ligand mismatching on 10-year graft survival in HLA-A, -B, -DR compatible kidney transplants. Further analysis did not reveal a significant effect of recipient activating/inhibitory KIR or KIR genotypes on graft survival. Our data do not support the concept that KIR-HLA matching might serve as a tool to improve long-term renal allograft survival.

The wound watch: an objective staging system for wounds in the diabetic (db/db) mouse model

As in cancer biology, in wound healing there is a need for objective staging systems to decide for the best treatment and predictors of outcome. We developed in the diabetic (db/db) wound healing model, a staging system, the "wound watch," based on the quantification of angiogenesis and cell proliferation in open wounds. In chronic wounds, there is often a lack of cellular proliferation and angiogenesis that leads to impaired healing. The wound watch addresses this by quantifying the proliferative phase of wound healing in two dimensions (cellular division and angiogenesis). The results are plotted in a two-dimensional graph to monitor the course of healing and compare the response to different treatments.

Comparison of lyophilization, and freezing in honey as techniques to preserve cortical bone allografts used to repair experimental femoral defects in domestic adult cats

Cats with orthopedic conditions are a prominent part of the clinical work of veterinary. Conditions such as comminuted fractures, bone tumors and non-unions are often difficult to repair and may require the use of bone grafts for treatment. This study evaluated cortical bone allografts preserved in honey, frozen or lyophilized for correcting long bone defects created in the diaphysis of the right femur of domestic cats (n=24). In the control group (n=6), the defect was repaired using autogenous cortical bone graft. In the remaining animals (n=6/group), the defect was repaired with cortical bone allografts preserved in honey, frozen or lyophilized. Success of graft incorporation and length of time for consolidation were assessed through clinical, radiographic and histological evaluations performed up to 180 days. In the control, frozen, honey and lyophylized groups, respectively, success of graft incorporation was 91.6%, 83.3%, 75%, and 25%, with corresponding mean length of time for consolidation of 83.1, 78, 105 and 120 days. Incorporation percentage in the lyophilized group was significantly lower than in the frozen and control groups. In conclusion, bone grafts preserved in honey or frozen were effective for repairing cortical defects in the femurs of cats as compared to autogenous cortical bone grafts.

P2-09-02: Predicting Response to Bevacizumab in Primary Breast Cancer Using 18F-Fluorothymidina (FLT) and 18F-Misonidazole (MISO) Positron Emission/Computed Tomography (PET/CT) as Imaging Biomarkers

Background: To investigate the hypothesis that early changes in tumor proliferation and hypoxic status induced by bevacizumab and assessed by imaging biomarkers might predict response to bevacizumab therapy.

Methods: 73 chemotherapy naïve, stage II-III breast cancer (BC) patients (pts) were enrolled in the training set of this phase II, single-arm, multicenter and prospective clinical trial from October 2009 until November 2010. Pts received single infusion of bevacizumab (15 mg/kg) (C1) 3 weeks prior to the beginning of neoadjuvant chemotherapy (NAC) consisting in 4 cycles of docetaxel (60 mg/mq), doxorubicin (50 mg/mq) and bevacizumab (15 mg/kg) every 21 days (C2-C5) following by surgery. Tumor proliferation and hypoxic status were evaluated using FLT and MISO PET/CT at baseline and 14–21 days after bevacizumab (C1). Standardized uptake values (SUV) for FLT and MISO and ratios to reference tissues, mediastinum (T/Me) or muscle (T/Mu), for MISO were calculated. Pathological response on surgical specimens was assessed according to Miller/Payne grading system. Pts with reduction in tumor cells &gt;30% (G3-G4-G5) or &lt;30% (G1-G2) were respectively considered as responders and no-responders. Association between pathological response, baseline and changes induced by bevacizumab (C1) in imaging biomarkers was analyzed using Mann-Whitney test. Receiver operating characteristic (ROC) curve was performed to test sensitivity and specificity of the biomarker found associated to response. Its value as independent predictor was tested in multivariate analysis using logistic regression. Results: Median baseline MISO and FLT SUV values in tumors were 1.2 (range 0.69−2.39) and 2.89 (range 0.97−7.18). Significant change after C1 was observed in FLT (2.7 vs 1.8, p&lt;0.001) but no in MISO uptake. Fifty-two (74%) pts achieved response (G3-G4-G5) whether 18 (24%) were considered as no responder (G1-G2); for 3 (4%) patients Miller/Payne tumor evaluation was not available. Response showed a trend toward an association with negative estrogen receptors (ER) expression (p=0.08) and triple negative tumors (11/73) (p=0.05). FLT SUV baseline and changes after C1 in MISO SUV, T/Mu and T/Me were all significantly associated with pathological response (p=0.057, 0.03, 0.016, 0.010). ER expression and T/Mu change remained significantly associated with response in multivariate analysis (OR=24.8, IC95% 1.8-334, p=0.01 and OR=0.95, IC 95% 0.92−0.99, p value=0.02). Decrease in MISO T/Mu uptake &gt;20% yielded a ROC curve area of 0.7 (95% CI: 0.56 - 0.85) with 94% sensitivity and 87% specificity. Conclusion: Bevacizumab determined a marked decrease in tumor proliferation. Interestingly, a decrease greater than 20% in tumor hypoxic status after C1 and assessed by MISO was found significantly associated with pathological response suggesting a potential value of early decrease in hypoxic tumor status as predictive biomarker of response. Bevacizumab, causing normalization of the tumor microvasculature, seems to potentiate the effect of cytotoxic agents on primary BC. A validation set is warranted to confirm these findings.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-09-02.

P2-08-05: Use of Dynamic Contrast-Enhanced MR Imaging To Predict Pathological Response in Primary Breast Cancer

Purpose: To investigate the effect of bevacizumab infusion on vascular parameters assessed by dynamic contrast-enhanced magnetic resonance (DCE-MR) imaging and to test their association with pathological response in primary breast cancer.

Materials and Methods: 73 patients (median age, 47 ys; age range, 29–70 ys) with biopsy-proven, previously untreated, primary breast cancer were recruited from October 2009 to November 2010 in this phase II, multicenter and non-randomized clinical trial. Patients (pts) received single infusion of bevacizumab (15 mg/kg) (C1) 3 weeks prior to the beginning of neoadjuvant chemotherapy consisting in 4 cycles of docetaxel (60 mg/mq), doxorubicin (50 mg/mq) and bevacizumab (15 mg/kg) every 21 days (C2-C5) following by surgery. All pts underwent DCE-MR imaging before and 14–21 days after C1. Quantitative and semiquantitative kinetic parameters were calculated at baseline and after C1, including the volume transfer constant (K(trans)), which primarily reflects the wash-in of the contrast agent, the backflow rate contrant (K(ep)), extracellular volume fraction (V(e)) and the initial area under the gadolinium concentration-time curve over 60 seconds (IAUGC(60)). Changes in the DCE-MRI kinetic parameters K(trans), K(ep), V(e) and IAUGC(60) were calculated and Wilcoxon test was used to assess significant effects induced by bevacizumab on kinetic parameters. Pathological response on surgical specimens after C5 was assessed according to Miller and Payne classification. Pts with tumor reduction &gt;30% were considered as responders (G3-G4-G5) whether tumor reduction &lt;30% were considered as no responders (G1-G2). DCE-MR imaging parameters and clinical-pathological characteristics were correlated with pathological response using Mann-Whitney test in univariate and logistic regression in multivariate analyses. Receiver operating curves (ROC) was used to define the best cut-off of the parameter found associated with pathological response.

Results: DCE-MRI was performed before (n=72) and after (n=71) C1. K(trans), K(ep), V(e) and IAUCG(60) values were significantly different at the baseline and after C1 (p&lt;0.01). Median changes were, respectively, −51, −101, −52.5 and −4.8. Fifty-two (74%) pts achieved response (G3-G4-G5) after C5 whether 18 (24%) were considered as no responder (G1-G2); for 3 (4%) patients Miller/Payne tumor evaluation was not available. At univariate analysis, negative estrogen receptor (ER) status and higher post-C1 K(ep) (p=.057) showed a trend toward an association with response. At multivariate analysis, only ER status remains a significant predictor of response (p= .04). Area under ROC curve for K(ep) was 0.65 (IC95% 0.05−0.8, p=.057)

Conclusion: Bevacizumab affects tumor vasculature, perfusion and permeability as showed by the significantly reduction in all kinetic vasculature parameters obtained in DCE-MR imaging after C1. However, in our population these changes were not associated with pathological response. On the other hand, backflow rate constant, K(ep), a perfusion-related parameter derived from DCE-MRI yielded after C1 major than 80, may be associated with higher pathological response with a specificity of 88% and sensitivity of 90%. Future studies are warranted to confirm these findings.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-08-05.

P5-13-04: Changes in Phosphorylation Status at VEGFR2 and Basal Tumor Hypoxic Volume Assessed by Misonidazol (MISO) Positron Emission Tomography (PET/CT) as Potential Biomarkers for Predicting Response to Bevacizumab in Breast Cancer

Background: To evaluate the expression of novel putative biomarkers as predictors of benefit from bevacizumab in stage II-III, previously untreated breast cancers (BC) patients (pts) in the context of a phase II, single-arm, multicenter and prospective clinical trial. To address this aim, we examined baseline and induced changes after a single bevacizumab administration as potential early predictors of response. Methods: Pts received a single infusion of bevacizumab (15 mg/kg) (C1) 3 weeks prior to the beginning of neoadjuvant chemotherapy consisting in 4 cycles of docetaxel (60 mg/mq), doxorubicin (50 mg/mq) and bevacizumab (15 mg/kg) every 21 days (C2-C5) following by surgery. Early assessment of tumor changes was performed by paired tumor-biopsies and MISO PET/CT before and 14–21 days after bevacizumab administration (C1). Biomarker expression was assessed by immunohistochemistry (IHC) (Ki67, CD31, CD31/Ki67, VEGFR2, pVEGFR2 [Y951]) on formalin-fixed, paraffin-embedded tissue before and after bevacizumab infusion (C1). MISO SUV and tumor volume depicted by PET were calculated. Pathological response on surgical specimens was assessed according to Miller/Payne classification. Pts with tumor reduction &gt;90% were considered as best responders (G4-G5) whether tumor reduction &lt;90% were considered as no responders. Association between pathological response, IHC and MISO biomarkers was analyzed using Mann-Whitney test. ROC curve was performed to test sensibility and specificity of the biomarker found significantly associated with response and its value as independent predictor was tested in the multivariate analysis using logistic regression.

Results: This analysis was performed on the training set including 73 patients (49 yr, range 29–70). Twenty (27%) patients obtained best response (G4-G5) whether 50 (68%) were considered as no responder (G1-G2-G3). Response was associated with negative estrogen receptors expression (p=0.02) and high Ki67 basal and after C1 expression (p=0.009 and p=0.01). Six (54%) of triple negative tumors were responders (p=0.05). Interestingly, change in pVEGFR2 [Y951] staining induced by bevacizumab administration and basaline MISO tumor volume was found significantly associated with response (p=0.03 and 0.057). Decrease in the phosphorilation status of VEGFR2 (Y951) &gt;70% yielded a receiver operating characteristic (ROC) curve area of 0.681 (95% CI: 0.536 — 0.825) with 84% sensitivity and 95% specificity. The positive and negative predictive values for this marker were 60% and 64%, respectively. The change in phosphorilation status of VEGFR2p remains a significant predictor biomarker of response in multivariate analysis (OR=0.9, IC%95 0.96−0.99, p=0.04) after adjusting for clinical-pathological characteristics.

Conclusion: These findings underline the potential value of early decrease in phosphorilation status of VEGFR2 after bevacizumab infusion as predictive biomarker of response to anti-angiogenic therapy in breast cancer. Moreover, tumor hypoxic volume obtained by MISO might be associated with response. A validation set is warranted to confirm these findings.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-13-04.

Reassessing the impact of donor HLA-C genotype on long-term liver transplant survival

HLA-C is the major inhibitory ligand for killer immunoglobulin-like receptors (KIRs) that are expressed on natural killer (NK) cells. Based on their KIR specificity, HLA-C alleles can be divided into two groups, termed HLA-C1 and HLA-C2. Donor HLA-C group has recently been identified by Hanvesakul et al. (Am J Transplant 2008) as a critical determinant of clinical outcome following liver transplantation: Possession of at least one HLA-C group 2 allele by the donor was associated with significantly improved long-term graft and patient survival, presumably due to an inhibition of host NK cell function. To verify this study, we performed genotyping of 913 deceased liver donors for the relevant KIR epitopes of HLA-C and correlated the presence or absence of donor HLA-C2 genotype with graft and patient survival. In our study, donor HLA-C2 genotype had no impact on 10-year graft or patient survival. We cannot confirm a major role of donor HLA-C2 genotype on long-term allograft survival after liver transplantation.

Balanced left ventricular myocardial SSFP-tagging at 1.5T and 3T

The purpose of the study was to evaluate the performance of steady-state free precession (SSFP)-tagging at 1.5T and 3T and to define the ideal settings with respect to optimized tag contrast throughout the cardiac cycle for both field strengths. To identify optimal imaging parameters data acquisition was repeated for different flip angles. Left ventricular tag-tissue contrast, tag fading times, tag persistence, and myocardial signal-to-noise ratio (SNR) were quantified in basal, mid-ventricular, and apical slice locations. To assess the effect of field strength on image quality and artifact level, additional semiquantitative image grading was performed by two experienced readers. SSFP-tagging at 3T proved superior to 1.5T and provided significantly enhanced tag persistence and myocardial SNR while maintaining overall image quality and artifact level. The definition of a tag quality index demonstrated optimal SSFP-tagging performance for a flip angle of 20 degrees . Diastolic tag visibility was improved at 3T and resulted in enhanced average tag persistence of 789 +/- 128 ms compared to 523 +/- 40 ms at 1.5T. For SSFP-tagging at 3T the combination of T(1) lengthening and superior myocardial SNR is highly promising and has the potential to improve the depiction of tagged myocardial function throughout the entire cardiac cycle.

Stability of the biodiversity of the surface consortia of Gubbeen, a red-smear cheese

A total of 1,052 bacteria and 828 yeasts were isolated from the surface flora of 6 batches of Gubbeen cheese made in 1996-1997 and 2002-2003. Stability of the microflora was evaluated over time and also during ripening at 4, 10, and 16 d (batches 4, 5, and 6) or at 4, 16, 23, and 37 d (batches 1, 2, and 3). Bacteria were identified using pulsed-field gel electrophoresis, repetitive extragenic palindromic-PCR, and 16S rRNA gene sequencing, and yeasts were identified by Fourier transform infrared spectroscopy. The bacteria included at least 17 species, of which the most common were Staphylococcus saprophyticus (316 isolates), Corynebacterium casei (248 isolates), Brevibacterium aurantiacum (187 isolates), Corynebacterium variabile (146 isolates), Microbacterium gubbeenense (55 isolates), Staphylococcus equorum/cohnii (31 isolates), and Psychrobacter spp. (26 isolates). The most common yeasts were Debaryomyces hansenii (624 isolates), Candida catenulata (135 isolates), and Candida lusitaniae (62 isolates). In all batches of cheese except batch 2, a progression of bacteria was observed, with staphylococci dominating the early stages of ripening and coryneforms the later stages. No progression of yeast was found. Pulsed-field gel electrophoresis showed that several different strains of the 5 important species of bacteria were present, but generally only one predominated. The commercial strains used for smearing the cheese were recovered, but only in very small numbers early in ripening. Four species, B. aurantiacum, C. casei, C. variabile, and Staph. saprophyticus, were found on all batches of cheese, but their relative importance varied considerably. The results imply that significant variation occurs in the surface microflora of cheese.

Identification of two novel HLA alleles, HLA-A*02010103 and HLA-B*4455, and characterization of the complete genomic sequence of HLA-A*290201

We describe two novel human leukocyte antigen (HLA) alleles, HLA-A*02010103 and HLA-B*4455, that were discovered in two unrelated Caucasian individuals. In addition, we report the full-length genomic sequence of HLA-A*290201. Compared with HLA-A*02010101, HLA-A*02010103 has three nucleotide (nt) changes within intron 1, which is altered to a sequence typical of the HLA-A*23/A*24 allele group. In HLA-B*4455, an nt exchange occurred in codon 9 of HLA-B*44020101, resulting in a change of the amino acid coding from tyrosine to histidine. We sequenced HLA-A*290201 from nt -108 to nt 2922, encompassing all exons and introns as well as parts of the 5' and 3' untranslated regions. Previously, the full-length genomic sequence was known only for HLA-A*29010101, which is found at a lower frequency in Caucasians than HLA-A*290201.

Identification and characterization of three novel HLA alleles, HLA-A*240214, HLA-A*3215 and HLA-DQB1*060302

We describe three novel human leukocyte antigen (HLA) alleles found in three different Caucasians, HLA-A*240214, HLA-A*3215 and HLA-DQB1*060302. As compared with HLA-A*24020101, HLA-A*240214 has a synonymous nucleotide (nt) exchange in codon 132. HLA-A*240214 may have arisen from intergenic recombination between HLA-A*24020101 and an HLA-B or HLA-C allele. The second novel allele, HLA-A*3215, has three nucleotide exchanges as compared with HLA-A*320101. These variations result in amino acid exchanges in codons 62 and 63, generating the public epitope of the serological HLA-A10 group. The third novel allele, HLA-DQB1*060302, has one synonymous nucleotide exchange within codon 38 as compared with HLA-DQB1*060301. In a family segregation study, we found that HLA-DQB1*060302, similar to the known HLA-DQB1*060301 allele, cosegregates with HLA-DRB1*1301.

Role of minor histocompatibility antigens in renal transplantation

In hematopoietic stem cell transplantation (HSCT), disparities between recipients and donors for minor histocompatibility antigens (mHags) have been shown to be related to graft-versus-host disease (GVHD) and graft-versus-leukemia (GVL) effects. We investigated the effect of mHag mismatches on kidney allograft survival. Out of 33 785 kidney transplants on which DNA and clinical data were available to the Collaborative Transplant Study (CTS), 702 recipient/donor pairs could be identified as HLA-A, -B and -DRB1 matched first transplants of Caucasian origin. These pairs were typed for genetic polymorphisms of the mHags HA-1, HA-2, HA-3, HA-8, HB-1, ACC-1 and UGT2B17. Because mHags are presented in an HLA-restricted manner, only HLA-A*02 positive pairs were included in the analysis of HA-1, HA-2 and HA-8. Similarly, only HLA-A*01, HLA-B*44 and HLA-A*24 positive pairs were considered for the evaluation of HA-3, HB-1 and ACC-1, respectively, whereas UGT2B17 compatible transplants were assessed in HLA-A*29 and HLA-B*44 positive pairs. None of the mHag disparities showed a statistically significant effect on death-censored 5-year graft survival. This report represents the first large-scale study on the relevance of mHags in kidney transplantation.