Abstract 509: Tumor inflammation signature (TIS) in residual disease is associated with survival in breast cancer patients with high risk of recurrence

Background: The assessment of tumor inflammation signature (TIS) quantifies the adaptive immune response in the tumor microenvironment and is emerging as a predictor of clinical benefit in breast cancer. In this study we evaluated the ability of TIS to be a prognostic biomarker of survival benefit in patients with moderated and high residual disease after neoadjuvant chemotherapy (NAC) in breast cancer patients and its correlation with residual TILS after NAC.

Methods: We analyzed 46 samples of residual disease of breast cancer patients who received NAC and were under surgery between 2013 - 2018, with high risk of recurrence defined as Residual Cancer Burden (RCB) group II and III. TIS signature was evaluated using the Research Use Only version of 18-gen signature algorithm. Median of TIS score was 5.88, TIS score were categorized in four groups by quartiles and defined as low TIS score (lower quartile, score ≤ 4.82) and high TIS score (score > 4.82). In addition, we quantified the percentage of stromal TILS in residual disease, categorizing level of TILS in high and low level using median (20%) as a cut-off. Survival analysis was performed with Kaplan-Meier method and the associations with Cox regression model. Correlation between TIS and TILS was performed whit Pearson coefficient. Clinical data was collected of medical records.

Results: The median age at diagnosis was 50 years (26y - 78y), 65.2% of patients were Luminal B subtype, 63% were clinical stage IIIB, 26.2% were RCB II and 73.9% RCB III. No correlation between TIS score and percentage of stromal TILS was founded (p = 0.264). After median follow-up of 60 months, estimated median PFS for high TIS score was 71.7 vs 18.2 months for low score (HR = 0.28, 95% CI [0.13-0.64], p = 0.002), and estimated median OS for high TIS score was non-reached vs 40.9 months for low score (HR = 0.28, 95% CI [0.11-0.68], p = 0.005). Did not found differences in PFS (p = 0.408) and OS (p = 0.773) by level of TILS.

Conclusions: High TIS score in moderated/high residual disease after neoadjuvant chemotherapy is associated with survival benefit expressed in prolonged PFS and OS. Level of TILS in residual disease did not show differences in survival and its percentage did not have correlation with TIS score.

Funding: FONDECYT-198-2015/280-INNOVATEPERU-EC-2017.

Citation Format: Marco Galvez-Nino, Miluska Castillo, Luis Bernabe, Nancy Suarez, Joselyn Sanchez, Katia Roque, Silvia Neciosup, Henry Gomez, Carlos Castaneda. Tumor inflammation signature (TIS) in residual disease is associated with survival in breast cancer patients with high risk of recurrence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 509.

The tale of TILs in breast cancer: A report from The International Immuno-Oncology Biomarker Working Group

The advent of immune-checkpoint inhibitors (ICI) in modern oncology has significantly improved survival in several cancer settings. A subgroup of women with breast cancer (BC) has immunogenic infiltration of lymphocytes with expression of programmed death-ligand 1 (PD-L1). These patients may potentially benefit from ICI targeting the programmed death 1 (PD-1)/PD-L1 signaling axis. The use of tumor-infiltrating lymphocytes (TILs) as predictive and prognostic biomarkers has been under intense examination. Emerging data suggest that TILs are associated with response to both cytotoxic treatments and immunotherapy, particularly for patients with triple-negative BC. In this review from The International Immuno-Oncology Biomarker Working Group, we discuss (a) the biological understanding of TILs, (b) their analytical and clinical validity and efforts toward the clinical utility in BC, and (c) the current status of PD-L1 and TIL testing across different continents, including experiences from low-to-middle-income countries, incorporating also the view of a patient advocate. This information will help set the stage for future approaches to optimize the understanding and clinical utilization of TIL analysis in patients with BC.

Thoroughbred stallion fertility is significantly associated with FKBP6 genotype but not with inbreeding or the contribution of a leading sire

This is a follow-up study to validate the previously detected association of the FKBP6 gene with stallion subfertility. Using a select cohort of 150 Thoroughbred stallions with detailed breeding records, we confirm significant association (P < 0.0001) between low per-cycle pregnancy rates (≤50%) and a combined A/A-A/A genotype of SNPs chr13:11 353 372G>A and chr13:11 353 436A>C in FKBP6 exon 5. We also show that stallion subfertility and the combined genotype A/A-A/A are not associated with the level of genetic diversity based on 12 autosomal microsatellite markers, or with pedigree-based inbreeding rate, or the extent of contribution of a leading Thoroughbred sire, Northern Dancer, in a stallion's pedigree. We develop a TaqMan allelic discrimination assay for the two SNPs to facilitate accurate and high-throughput genotyping. We determine allele, genotype and combined genotype frequencies of FKBP6 exon 5 SNPs in a global cohort of 518 Thoroughbreds (76% stallions or geldings and 24% mares) and show that the frequency of the A/A-A/A genotype is 4%. Because there is no similar association between the FKBP6 exon 5 genotype and stallion subfertility in Hanoverians, we suggest that the two SNPs are not causative but rather tagging a breed-specific haplotype with genetic variants unique to Thoroughbreds. Further WGS-based research is needed to identify the molecular causes underlying the observed genotype-phenotype association in Thoroughbred stallions.

Abstract P1-10-22: Predictive biomarkers of survival after neoadjuvant chemotherapy for breast cancer

Introduction: The use of neoadjuvant chemotherapy (NAC) has become the standard of care in non-metastatic breast cancer patients meaning an improvement of tumor regression rates with a high impact on survival especially in patients who achieve pathological complete response (pCR). Predictive biomarkers of survival acquire more relevance in the setting of patients who don’t achieve complete response allowing us to design strategies based on the response evaluation. This study aimed to evaluate the predictive value of the NAC response represented by residual cancer burden (RCB) and tumor-infiltrating lymphocytes in residual disease (RD TILs). Methods: We analyze non-metastatic breast cancer patients diagnosed at Instituto Nacional de Enfermedades Neoplasicas (INEN), Lima-Peru who received NAC and were under surgery from 2016 to 2019, we performed a prospective evaluation of RCB and the level of stromal RD TILS by hematoxylin and eosin (H&E), CD-3 and CD-8 by immunohistochemistry in a subgroup of patients, we choose the median of percentage as a cut-off. Epidemiologic and clinic-pathological data were collected from clinical files. Survival analysis was calculated by using Kaplan-Meier method. Results: During the study period, we analyzed 271 NAC cases, median of age of diagnosis was 51 years, most common molecular subtype was Luminal B (56.5%) followed by Triple Negative (24.4%), 124 (45.8%) patients were at clinical stage IIIB followed by 54 (19.9%) IIB. 226 (83.4%) patients didn’t achieve pCR, most of them achieved RCB class III (40.6%) followed by RCB class II (37.6%). Among these we evaluated RD TILs in 42 patients. 54.8% of patients had RD TILs level greater than 30%, 53.3% had CD-3 level greater than 60% and 51.2% a level of CD-8 greater than 40%. Median PFS was 42 months (range 15.6 - 68) and estimated 3-years OS was 95.5%. We found significative difference between the RCB class and PFS (p=0.001) and OS (p=0.035), no differences between the level of stromal RD TILs, CD-3 or CD-8 with PFS or OS was found. Conclusion: Results from this cohort provide evidence for the benefit of NAC, in this setting RCB had a significative predictive value for breast cancer recurrence and survival, however, the level of RD TILs, CD-3 and CD-8 didn’t show differences on survival maybe by the number of cases. This work was supported by CONCYTEC (contract No. 198-2015-CONCYTEC) Keywords: Breast cancer, Neoadjuvant, Residual cancer burden, TILs, progression-free survival.

Citation Format: Marco Galvez-Nino, Katia Roque, Luis Angel Bernabe, Miluska Castillo, Joselyn Sanchez, Maria Landa Baella, Gabriela Calderon, Miguel De la Cruz, Jorge Dunstan, Julio Abugatas, Jose Cotrina, Carlos Castaneda, Henry Gomez. Predictive biomarkers of survival after neoadjuvant chemotherapy for breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P1-10-22.

Abstract 4564: Tumor infiltrating lymphocytes are associated with p16 protein expression in acral lentiginous melanoma

Background: The loss of function of gene p16(INK4a)/CDKN2 is associated with the development of several neoplasm and tumor progression, likewise, the level of tumor infiltrating lymphocytes is a predictive and prognostic biomarker of survival. This study aims to evaluate the association between composition of tumor infiltrating lymphocytes (TILs) and expression of p16 in acral lentiginous melanoma (ALM), and their impact on prognosis.

Materials and methods: A cohort of 148 surgical pathology specimens of ALM was studied. TILs were evaluated by immunohistochemical detection of CD3 and CD8, along with CD20, CD4, CD68, and CD163 in a subset of 43 cases, likewise, we classify the level of TILs in grades by combining density and distribution. p16 protein expression by immunohistochemistry was also investigated in all cases.

Results: The median age was 66 years, median Breslow thickness was 6.0 mm, Grade III of TILs was found in 28.4% and lymph nodes were involved in 44.6%. Breslow thickness (p&lt;0.001), stage I-II (p&lt;0.001), negative lymph nodes (p&lt;0.001) and &lt;10% p16 (p&lt;0.001) were associated with longer survival. Grade III of TILs was associated with thinner Breslow thickness (p=0.008) and lower mitosis (p=0.047). A higher density of CD3 TILs was associated with male gender (p=0.008), thinner Breslow thickness (p=0.047), negative lymph node (p=0.031), early stage (p=0.046), and p16 nuclear expression of &gt;10% (p=0.045). Higher CD8 TIL was associated with &gt;p16 (p=0.03). Survival analysis found that longer survival doesn’t associated with high grade of TILs (p=0.094). Levels of CD3+ and CD8+ cells were correlated with those of CD4+, CD20+, CD68+ and CD163+ immune cells.

Conclusions: Loss of expression of p16 is associated with lower levels of CD3+ and CD8+ TIL, indicating a probable relationship between p16 and TILs immune response in ALM.

Citation Format: Marco A. Galvez Nino, Miluska Castillo, Luis A. Bernabe, sandro Casavilca, Valeria Villegas, Joselyn Sanchez, Jorge Dunstan, Julio Abugatas, Carlos Castaneda, Henry Gomez. Tumor infiltrating lymphocytes are associated with p16 protein expression in acral lentiginous melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4564.

Prognostic implications of residual disease tumor-infiltrating lymphocytes and residual cancer burden in triple-negative breast cancer patients after neoadjuvant chemotherapy

BACKGROUND

For primary triple-negative breast cancer (TNBC) treated with neoadjuvant chemotherapy (NAC), higher pretreatment tumor-infiltrating lymphocytes (TILs) correlates with increased pathologic complete response (pCR) rates, and improved survival. We evaluated the added prognostic value of residual disease (RD) TILs to residual cancer burden (RCB) in predicting survival post-NAC.

PATIENTS AND METHODS

We combined four TNBC NAC patient cohorts who did not achieve pCR. RD TILs were investigated for associations with recurrence-free survival (RFS), and overall survival (OS) using Cox models with stromal TILs as a continuous variable (per 10% increment). The likelihood ratio test was used to evaluate added prognostic value of RD TILs.

RESULTS

A total of 375 RD TNBC samples were evaluable for TILs and RCB. The median age was 50 years, with 62% receiving anthracycline/taxane chemotherapy. The RCB class after NAC was 11%, 50%, and 39% for I, II, and III, respectively. The median RD TIL level was 20% (IQR 10-40). There was a positive correlation between RD TIL levels and CD8+ T-cell density (ρ = 0.41). TIL levels were significantly lower with increasing post-NAC tumor (P = 0.005), nodal stage (P = 0.032), but did not differ by RCB class (P = 0.84). Higher RD TILs were significantly associated with improved RFS (HR: 0.86; 95% CI 0.79-0.92; P < 0.001), and improved OS (HR: 0.87; 95% CI 0.80-0.94; P < 0.001), and remained significant predictors in multivariate analysis (RFS P = 0.032; OS P = 0.038 for OS). RD TILs added significant prognostic value to multivariate models including RCB class (P < 0.001 for RFS; P = 0.021 for OS). The positive prognostic effect of RD TILs significantly differed by RCB class for RFS (PInt=0.003) and OS (PInt=0.008) with a greater magnitude of positive effect observed for RCB class II than class III.

CONCLUSIONS

TIL levels in TNBC RD are significantly associated with improved RFS and OS and add further prognostic information to RCB class, particularly in RCB class II.

Abstract 3793: Immune cells in gastric cancer

Introduction: Role of TIL and interaction with H. pylori infection is not understood in Gastric Cancer.

Methods: Gastric tissue samples were retrospectively collected from 50 patients who were refereed to surgery at Instituto Nacional de Enfermedades Neoplasicas between 2011 and 2012. We prospectively evaluated the distribution and density of tumor-infiltrating lymphocytes (TIL) as well as the presence of H. pylori. An evaluation of the role of the density of different subpopulations of infiltrating immune cells in tissue TMA was additionally performed. Clinicopathological data were collected from medical and pathology reports. Kaplan-Meier estimation curves overall survival (OS) was applied. A p-value ≤0.05 was considered statistically significant.

Results: Median age was 52 years and 50% were male, most were HG-3 (83%), Lauren classification (76%) and clinical stage III (50%). Most cases went to subtotal gastrectomy (64%). H. pylori was present in 34% (17/49) and most frequent density was moderate (++) (10/49).

Intratumoral TIL mild (92%) and bandlike infiltration (68%).

Median percentage of intratumoral CD3, CD4, CD8, CD20, CD68 and CD163 TILs in 5 HPF were 12.00±0.108, 1.55±0.017, 7.96±0.093, 1.34±0.057, 12.30±.054 and 8.88±0.069, respectively.

No significant association between immune cell subpopulation density and features was found, however it was a trend to association for: Older age and CD163 (p=0.184), male sex and CD8 (p=0.166) and CD4 (p=0.171), poorly differentiated HG and CD4 (p=0.071), early stage and CD4 (p=0.084), diffuse Lauren classification and CD4 (p=0.13), and H. pylori 0&+/+++ and CD68 (p=0.171).

The median follow-up was 4.7 years (CI95%: 4.5-5.0), median survival was 1.7 years (CI95%. 0.6-2.9). Earlier clinical stage (p=0.003), non-lymphatic vascular invasion (p=0.024) and absence of node involvement (p=0.018), early Bormann classification (p=0.030) and absence of metastasis (p=0.029) were associates to survival. In relation to the types of TILs, CD3 (&lt;27.5, p=0.051), CD4 (&lt;2.6, p=0.015), CD8 (&gt;6.2, p=0.049), and CD4/CD8 (&lt;0.31, p=0.006) were associated with poor survival. However, in the Cox model age (&gt;60yr HR: 5.1) Bormann (IV, HR: 22.8), NLR (&lt;2.13, HR: 29.2), LMR (&gt;3.86, HR: 19.8) and CD4/CD8 (&lt;0.31, HR: 10.3) were associated with poor prognosis.Conclusion: Patients with NLR and CD4/CD8 TIL high had better survival. These results suggest the prognostic implications of biomarkers and type of TIL in patients with AGC that could be used in clinical practice.

Keywords: Gastric cancer, tumor-infiltrating lymphocytes, H. pylori

This study was supported by the CIENCIACTIVA-CONCYTEC, under the contract #197-2015-FONDECYT

Citation Format: Carlos Castaneda, Miluska Castillo, Luis Bernabé Monsalve, Joselyn Sanchez Sifuentes, Eduardo Payet Meza, Eloy Ruiz, Fernando Barreda Bolaños, Manuel Chumpitaz La Rosa Sanchez, Brayam Felix, Katherine Tello, Claudio Flores, Carlos Chavez, Ivan Chavez Passiuri. Immune cells in gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3793.

Abstract P6-15-04: Characterization of tumor infiltrating lymphocytes and its association response in breast cancer

Background: The magnitude of tumor infiltrating lymphocytes (TIL) is a predictor of good prognosis in the context of neoadyuvant chemotherapy (NAC) in breast cancer, and is expressed in the capacity to achieve a pathological complete response (pCR) and therefore to obtain a major survival. The characteristics of TIL are influenced of different clinical and pathological features as well as its predictive value. The goal of this study is to define the different associations between level of stromal (sTIL) and interstitial (iTIL) tumor infiltrating lymphocytes and pathological and clinical feature of breast cancer. Methods: The level of TIL was analyzed in 483 patients diagnosed with breast cancer of the Instituto Nacional de Enfermedades Neoplasicas from 2003 to 2014. We evaluate patient characteristics such as age, clinical stage, histological subtype and grade, clinical T, N and M, presence of estrogen (ER) and progesterone (PgR) receptors, HER-2 expression and molecular subtype as well as pathological response. Results: We found a positive association between sTIL and iTIL proportion and histological grade (G1-2 vs G3, p&lt;0.05 and p&lt;0.05 respectively), hormone receptor (ER- vs ER+PgR- vs ER+PgR+, p&lt;0.05 and p=0.001 respectively), molecular subtype (Luminal A vs Luminal B vs HER2 vs Triple Negative (TN), p&lt;0.05 and p=0.002 respectively), clinical N (positive vs negative, p=0.006 and p&lt;0.05 respectively). Also we found association between sTIL with lymph nodes after surgery (negative vs positive, p=0.028) and pathological response (pCR vs &lt;pCR, p=0.018), there was no association between sTIL and iTIL with age, histological subtype, clinical T and M. Conclusions: The level of tumor infiltrating lymphocytes are affected by different clinical and pathological features, they are present in both lobular and ductal breast cancer without significant difference; higher level of TIL are associated with high histological grade, ER-, TNBC and high clinical N to diagnosis; and specially sTIL are associated with to achieve a negative lymph node after NAC and obtain a pathological complete response.

Citation Format: Galvez M, Castaneda C, Villegas V. Characterization of tumor infiltrating lymphocytes and its association response in breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-15-04.

Abstract 4003: Acral lentiginous melanoma and infiltrating lymphocytes in a Latin American population

Background: Acral lentiginous melanoma (ALM) is unusual in Caucasian but is the most common subtype in Hispanic populations, and has been associated to poor prognosis. Herein we compare clinicopathological features associated to ALM in a Latin-American population and prospectively evaluate its association with tumor infiltrating lymphocytes (TIL).

Patients and Methods: All patients with melanoma presenting from 2005 to 2012 at Instituto Nacional de Enfermedades Neoplasicas in Lima, Peru, were retrospectively identified. Analysis of association between clinicopathological features and ALM was performed. Survival analysis compared the outcome of ALM to whole group and extremity NALM. We performed prospective evaluation of TIL following Azimi et al recently presented classification.

Results: A total of 537 ALM and 287 NALM cases were identified. Older age (p= 0.02), thicker Breslow (p= 0.008), positive lymph node (p= 0.051) and ulceration (p&lt;0.001) were found to be more frequent in ALM. Acral had worse OS compared with both whole group (p= 0.04) and extremity NALM (p &lt;0.001). Stage I-II patients had a median OS of 5.3 (95%CI: 4.3-6.2) for ALM and 9.2 (95% CI: 5.0 - 7.0) for extremity NALM (p=0.016). TIL was prospectively evaluated in 490 cases, and Grade 0-1, II and III of TIL represented 44.7%, 33.6% and 27.1%, respectively. Higher TIL grade was associated to less Breslow thickness (p= 0.021), less mitosis index and NAM. Higher TIL grade was also associated to better OS (p&lt; 0.001)

Conclusion: ALM is highly prevalent in Latin-America and carry poor outcome. Lower TIL levels was associated to poor outcome and ALM.

Citation Format: Carlos Castaneda, Carlos Torres-Cabala, Sandro Casavilca, Miluska Castillo, Valeria Villegas, Joselyn Sanchez, Claudio Flores, Henry Gomez, Tatiana Vidaurre. Acral lentiginous melanoma and infiltrating lymphocytes in a Latin American population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4003. doi:10.1158/1538-7445.AM2017-4003

Abstract 2394: Subpopulation of infiltrating lymphocyte and MGMT methylation in brain tumor prognosis

Background: Clinicopathological features including MGMT methylation have been correlated to prognosis in Glioblastoma (GBM). Tumor infiltrating lymphocytes (TILs) are predictive of clinical outcome in different malignancies. We evaluated association between clinicopathological features including MGMT methylation and IHC infiltrating immune cell subpopulations in 43 resected GBM cases who came from 2008 to 2013.

Methods: A prospective evaluation of TIL (CD3, CD4, CD8 and CD20) and macrophages (CD68 and CD163) through H&E was performed by a pathologist and evaluated Immune cell subpopulations was evaluated through scanning, and software analysis (BX63 Olympus and TissueMorph-Visionpharm) with pathologist support. MGMT evaluation was prospectively performed by bisulphyte PCR test in paraffin samples.

Results: Median age was 47.9 y, men (51.2%), Karnofsky scale 90% (62.8%), median tumor size of 5.1 cm, and partial/ complete tumor resection (22/21). Methylation MGMT test was performed in 31 cases and 17 showed un- methylated, 4 partial methylated and 10 methylated. TILs evaluation by HE showed low- intensity (29 cases), middle- intensity (1) and high- intensity level (9). Pattern of distribution was focal (9 cases), multi- focal (13) and diffuse (17). Median CD3, CD4, CD8, CD20, CD68 and CD163 were 1.6%, 0.032%, 1.6%, 0.03%, 9.1% and 2.2% (regarding total cells), respectively. Higher CD163 level was associated to male (p=0.03) and larger size (p=0.05). Higher levels of CD8 was associated to larger size (p=0.05). Higher CD8 and CD20 was associated to unmethylated MGMT (p=0.041 and 0.013). Median follow- up was 14 months. Only total resection (p&lt;0.05) and MGMT methylation (p&lt;0.05) was associated to outcome. Lymphocyte infiltration (H&E) was not associated to outcome: Lymphocyte intensity (p=0.703), distribution (p=0.61). Longer OS was associated to lower CD4 levels (p=0.01).

Conclusion: Tumor Infiltrating immune cell are not common in GBM, CD8 and CD20 was associated to unmethylation, and CD4 and MGMT methylation were associated to prognosis.

Citation Format: Carlos Castaneda, Miluska Castillo, Carolina Belmar-Lopez, Sandro Casavilca, Luis Angel Bernabe, Tatiana Vidaurre. Subpopulation of infiltrating lymphocyte and MGMT methylation in brain tumor prognosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2394. doi:10.1158/1538-7445.AM2017-2394

Mutational analysis of BRCA1 and BRCA2 genes in Peruvian families with hereditary breast and ovarian cancer

Background

Breast cancer is one of the most prevalent malignancies in the world. In Peru, breast cancer is the second cause of death among women. Five to ten percent of patients present a high genetic predisposition due to BRCA1 and BRCA2 germline mutations.

Methods

We performed a comprehensive analysis of BRCA1 and BRCA2 genes by Sanger sequencing and multiplex ligation‐dependent probe amplification (MLPA) to detect large rearrangements in patients from 18 families, which met the criteria for hereditary breast cancer.

Results

In this series, we found four pathogenic mutations, three previously reported (BRCA1: c.302‐1G>C and c.815_824dup10; BRCA2: c.5946delT) and a duplication of adenines in exon 15 in BRCA1 gene (c.4647_4648dupAA, ClinVar SCV000256598.1). We also found two exonic and four intronic variants of unknown significance and 28 polymorphic variants.

Conclusion

This is the first report to determine the spectrum of mutations in the BRCA1/BRCA2 genes in Peruvian families selected by clinical and genetic criteria. The alteration rate in BRCA1/BRCA2 with proven pathogenic mutation was 22.2% (4 out 18) and this finding could be influenced by the reduced sample size or clinical criteria. In addition, we found three known BRCA1/BRCA2 mutations and a BRCA1 c.4647_4648dupAA as a novel pathogenic mutation.

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

A phase I/II trial of ispinesib, a kinesin spindle protein (KSP) inhibitor, dosed q14d in patients with advanced breast cancer previously untreated with chemotherapy for metastatic disease or recurrence

1077

Background: KSP is a mitotic kinesin essential for cell cycle progression. Ispinesib, a selective KSP inhibitor, blocks mitotic spindle assembly with cell cycle arrest in mitosis and subsequent cell death. On a q21d schedule, the MTD was 18 mg/m2. In a phase II trial of ispinesib dosed at 18 mg/m2 q21d in patients (pts) with advanced breast cancer after anthracycline and taxane failure, the response rate was 4/45 (9%). This trial evaluates ispinesib given on d1 and d15 q28d, thus increasing dose density. Methods: In phase I of this phase I/II trial, DLT and MTD of ispinesib given d1 and d15 q28d will be determined. Eligibility criteria: advanced breast cancer; no prior chemotherapy (CT) except neoadjuvant or adjuvant and ≥ 1 yr elapsed since CT; no CNS metastases; ECOG 0–1. This is a standard 3+3 dose escalation trial design, starting at 10 mg/m2 and escalating based on tolerability in cycle (cy) 1. Pharmacokinetic data are collected in cy 1. Results: Phase I of the trial is ongoing. 16 pts were treated at 3 dose levels: 10 (n = 3), 12 (n = 6), and 14 mg/m2 (n = 7). 9 pts were stage IV; 11 were chemo-naïve; 5 had prior anthracycline and/or taxane; 4 were HER-2+ and 5 ER-, PR-, HER-2-. The most frequent toxicity was neutropenia. 88% of pts in cy 1 (grade 3/4 in 75%; no febrile neutropenia). Mild GI toxicity occurred in <37.5% of pts. There was no neuropathy or alopecia. At the 14 mg/m2 dose level, 2/7 pts had DLTs of transient grade 3 AST and ALT increases after cy 1 d15 dosing; both without increases upon retreatment; 1 in a pt with liver metastases; neither pt had significant increases in alkaline phosphatase or bilirubin. The 12 mg/m2 cohort was expanded to 6 pts without DLT. 3 pts had partial response (after 1 [n = 1] and 4 [n = 2] cy, respectively); 1 confirmed and ongoing after 8+ cy; 4 pts had stable disease ≥4 mo. Conclusions: Ispinesib appears to be well tolerated on a q14d dosing schedule at doses tested to date. A dose-density equal to that given in the prior phase II trial (0.86 mg/m2/d) was tolerated with the q14d schedule with preliminary evidence of efficacy. Further exploration of the 14 mg/m2 dose level is planned.

[Table: see text]

A phase I-II trial of Ispinesib, a kinesin spindle protein inhibitor, dosed every two weeks in patients with locally advanced or metastatic breast cancer previously untreated with chemotherapy for metastatic disease or recurrence

Abstract #2148

Kinesin Spindle Protein (KSP) is a mitotic kinesin essential for cell cycle progression. Ispinesib, a selective KSP inhibitor, blocks mitotic spindle assembly with cell cycle arrest in mitosis and subsequent cell death. When dosed on a q21d schedule, the maximum tolerated dose (MTD) was 18mg/m2 and neutropenia was the dose-limiting toxicity (DLT), with nadir at 7-10 d and recovery by d15. Activity was observed in a Phase II trial of ispinesib dosed at 18 mg/m2 q21d in patients (pts) with locally-advanced (LA) or metastatic breast cancer (MBC) after anthracycline and taxane failure (response rate 4/45 [9%]). This trial evaluates safety and efficacy of ispinesib in LA or MBC, given on d1 and d15 q28d, thus increasing dose density.&#x2028; Methods: This is a multicenter Phase I-II trial. In Phase I, DLT and MTD of ispinesib given d1 and d15 q28d will be determined. Eligibility criteria: LA or MBC; no prior chemotherapy (CT) except neoadjuvant or adjuvant and ≥ 1 year elapsed since CT; no CNS or leptomeningeal metastases; ECOG 0-1. This is a standard 3+3 dose escalation trial design, starting at 10 mg/m2 and escalating based on tolerability in Cycle 1. Pharmacokinetic data are collected on d1 and d15 of Cycle 1. Phase II of this trial will evaluate efficacy (response rate by RECIST) of ispinesib at the MTD.&#x2028; Results: Phase I of the trial is ongoing. To date, 13 pts have been treated at 3 dose levels: 10 (n=2; 2 cycles, n=1; 6 cycles), 12 (n=1; 1 cycle, n=2; 3 cycles) and 14 mg/m2 (n=7; Cycle 1 ongoing). Among the first 6 pts, 4 were Stage IV, 3 had prior neoadjuvant and 2 adjuvant CT; 2 were chemo-naïve. Four had prior anthracycline and 3 prior taxane. Biomarker status was ER+, PR+, HER2- (n=3), ER+, PR-, HER2- (n=1), ER-, PR-, HER2+ (n=3), ER-, PR-, HER2- (n=4), and unknown (n=2). Mean age was 55 yr; for the first 2 dose levels (n=6 pts), the most frequent toxicity was neutropenia (n=4). Other events included mild GI toxicity. No neuropathy or alopecia has been reported. The only grade 3 or 4 toxicity was neutropenia (n=2). At the 14 mg/m2 dose level, one DLT has been reported: a grade 3 transaminase (AST) elevation in a patient with liver metastases which resolved with a dose delay of 4 days. As a result, this cohort was expanded to include 6 evaluable pts. One additional patient at the 14mg/m2 dose had a dose delay of 5 days due to non-DLT neutropenia.&#x2028; Conclusions: Ispinesib appears to be well tolerated on a q2w dosing schedule at doses tested to date. A dose-density equal to that administered in the prior Phase II trial (0.86 mg/m2/day) was tolerated with the new q2w schedule. Dose escalation is ongoing.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2148.

Developing a valid evaluation for interpersonal and communication skills

OBJECTIVES

The Accreditation Council for Graduate Medical Education requires that residency programs evaluate the acquisition of six general competencies, including Interpersonal and Communication Skills (ICS). To develop a 360-degree method for accomplishing this, a semantic-differentiation matrix for various communication traits for nurses to evaluate physician ICS was developed. The authors sought to determine whether this evaluation method could discriminate between more experienced medical communicators (faculty) and less experienced medical communicators (residents).

METHODS

A 98-item questionnaire measured several communication dimensions by using an eight-element semantic-differentiation scale. In addition, global assessment ratings assessed nursing perceptions of physician ICS skills. This process was repeated for various clinical scenarios.

RESULTS

There were 26 nurse evaluators, 19 emergency medicine (EM) residents (EM2 and EM3), and 30 EM faculty. Each physician received five independent evaluations (total, 245 evaluations). All EM residents (EM2 and EM3) were compared with the EM faculty. All eight items on the semantic-differentiation scale were compared. Likewise, the global assessment scores were compared. In every category, the faculty scored higher (Mann-Whitney U: p < 0.001).

CONCLUSIONS

An evaluation process integrating a semantic-differentiation matrix was applied to various clinical scenarios (as well as global assessment items) and demonstrated discriminatory results. Faculty physicians scored significantly higher than resident physicians. The ability to provide discriminatory results is a requisite in the development of a valid evaluation process. The described semantic-differentiation matrix and global assessment questions may be valid measurements of ICS.

Mapping and initial analysis of human subtelomeric sequence assemblies

Physical mapping data were combined with public draft and finished sequences to derive subtelomeric sequence assemblies for each of the 41 genetically distinct human telomere regions. Sequence gaps that remain on the reference telomeres are generally small,well-defined,and for the most part,restricted to regions directly adjacent to the terminal (TTAGGG)n tract. Of the 20.66 Mb of subtelomeric DNA analyzed, 3.01 Mb are subtelomeric repeat sequences (Srpt),and an additional 2.11 Mb are segmental duplications. The subtelomeric sequence assemblies are enriched >25-fold in short,internal (TTAGGG)n-like sequences relative to the rest of the genome; a total of 114 (TTAGGG)n-like islands were found,55 within Srpt regions,35 within one-copy regions,11 at one-copy/Srpt or Srpt/segmental duplication boundaries,and 13 at the telomeric ends of assemblies. Transcripts were annotated in each assembly,noting their mapping coordinates relative to their respective telomere and whether they originate in duplicated DNA or single-copy DNA. A total of 697 transcripts were found in 15.53 Mb of one-copy DNA,76 transcripts in 2.11 Mb of segmentally duplicated DNA,and 168 transcripts in 3.01 Mb of Srpt sequence. This overall transcript density is similar (within approximately 10%) to that found genome-wide. Zinc finger-containing genes and olfactory receptor genes are duplicated within and between multiple telomere regions.

Resistance training to counteract the catabolism of a low-protein diet in patients with chronic renal insufficiency. A randomized, controlled trial

BACKGROUND

Chronic renal insufficiency leads to muscle wasting, which may be exacerbated by low-protein diets prescribed to delay disease progression. Resistance training increases protein utilization and muscle mass.

OBJECTIVE

To determine the efficacy of resistance training in improving protein utilization and muscle mass in patients with chronic renal insufficiency treated with a low-protein diet.

DESIGN

Randomized, controlled trial.

SETTING

Tufts University, Boston, Massachusetts.

PATIENTS

26 older patients with moderate renal insufficiency (17 men, 9 women) who had achieved stabilization on a low-protein diet.

INTERVENTION

During a run-in period of 2 to 8 weeks, patients were instructed and their adherence to the low-protein diet (0.6 g/kg of body weight per day) was evaluated. They were randomly assigned to a low-protein diet plus resistance training (n = 14) or a low-protein diet alone (n = 12) for 12 weeks.

MEASUREMENTS

Total body potassium, mid-thigh muscle area, type I and II muscle-fiber cross-sectional area, and protein turnover.

RESULTS

Mean protein intake was 0.64 +/- 0.07 g/kg per day after stabilization. Total body potassium and type I and II muscle-fiber cross-sectional areas increased in patients who performed resistance training by a mean (+/-SD) of 4% +/- 8%, 24% +/- 31%, and 22% +/- 29%, respectively, compared with those who did not. Leucine oxidation and serum prealbumin levels also improved significantly. Patients assigned to resistance training maintained body weight compared with those who were not. Improvement in muscle strength was significantly greater with resistance training (32% +/- 14%) than without (-13% +/- 20%) (P < 0.001).

CONCLUSION

By improving muscle mass, nutritional status, and function, resistance training seems to be effective against the catabolism of a low-protein diet and uremia in patients with renal failure.

The energy expenditure of postmenopausal women classified as restrained or unrestrained eaters

OBJECTIVE

Restrained eating is a common dietary practice among individuals who are attempting to prevent weight gain, but little is known about differences in energy physiology and regulation between restrained and unrestrained eaters. We investigated this issue in non-obese free-living postmenopausal women classified as long-term restrained (n=26) or unrestrained (n=34) eaters group matched for body mass index (BMI).

MEASUREMENTS

Measurements were made of total energy expenditure (TEE), resting energy expenditure (REE), body composition, reported leisure time activity, maximal aerobic capacity (VO2max) and weight change during the study period. In addition, physical activity level (PAL) and nonexercise activity thermogenesis (NEAT) were calculated from measured variables.

RESULTS

There were no significant differences between the groups in body composition, weight change, aerobic capacity or total leisure time activity. Relationships between fat-free mass (FFM) and both REE and TEE, and the relationship between work load and energy expenditure in the test of maximal oxygen consumption, were also not different between groups. However, restrained eaters had a significantly lower PAL (equal to TEE/REE, 1.72+/-0.04 vs 1.84+/-0.04, P<0.05). In addition, in multiple regression models predicting NEAT, NEAT was significantly lower in restrained eaters than unrestrained eaters and there was a positive relationship between NEAT and weight change in unrestrained eaters but no relationship in restrained eaters (P<0.05).

CONCLUSIONS

In contrast to a previous report, we found no significant difference in TEE between restrained and unrestrained eaters. PAL was slightly lower in restrained eaters, apparently due to reduced NEAT, and restrained eaters also lacked the positive association between NEAT and body weight change seen in unrestrained eaters. This latter finding, if confirmed in future studies, could help explain an increased susceptibility of restrained eaters to weight gain.

SPONSORSHIP

NIH grants AG12829, DK46124 and T32AG00209, and US Cooperative Agreement number 58-1950-9-001.

Marginal protein intake results in reduced plasma IGF-I levels and skeletal muscle fiber atrophy in elderly women

We investigated the effects of dietary protein on plasma IGF-I levels and muscle fiber cross-sectional area (CSA). Twelve healthy elderly women were randomly assigned to a weight-maintaining diet containing either 1.47 (marginal) or 2.94 (adequate) g protein/kg body cell mass (BCM)/d, (0.45 and 0.92 g/kg body weight/d, respectively) for 10wks. Plasma IGF-I levels and muscle fiber areas and distributions were evaluated at baseline and 10wks. After 10wks, both IGF-I and type I fiber CSA had declined significantly in subjects fed the marginal diet (30.1+/-2.1% and 32.7+/-7.9%, respectively) while they increased in those fed the adequate diet (19.5+/-7.0% and 22.3+/-7.5%, for IGF-I and type I CSA, respectively). The change in IGF-I was the only significantly associated with the change in type I fiber CSA (r2=0.70; p<0.03). These findings show that marginal dietary protein intakes will result in losses of muscle mass in the elderly and suggest a role for plasma IGF-I as a biochemical marker for the histological changes in skeletal muscle.

Type 2 diabetes is prevalent and poorly controlled among Hispanic elders of Caribbean origin

OBJECTIVES

We estimated prevalence and control of type 2 diabetes in Puerto Rican, Dominican, and non-Hispanic White (NHW) elders and associated them with sociodemographic and health behavior variables and with body mass index (BMI) and waist circumference.

METHODS

We used a cross-sectional analysis with a sample of Hispanic elders in Massachusetts and a comparison group of NHWs (1991-1997). The analysis included 379 Puerto Ricans, 113 Dominicans, and 164 NHWs, aged 60 to 96 years, with complete questionnaires and blood samples.

RESULTS

Type 2 diabetes was significantly more prevalent among Puerto Ricans (38%) and Dominicans (35%) than among NHWs (23%). Differences remained after covariates were adjusted for. Hispanics with diabetes were approximately 3 times more likely to use insulin than NHWs. Puerto Ricans were 2 times, and Dominicans 3 times, more likely to have glycosylated hemoglobin concentrations of 7% or above than NHWs. BMI and waist circumference were individually associated with diabetes. When included in the model together, waist circumference, but not BMI, remained independently associated with diabetes.

CONCLUSIONS

Ethnicity was more strongly associated with diabetes status and control than were socioeconomic or measured health behavior variables, suggesting that genetic or other culturally related factors may explain these differences.

Protein nutritional status and function are associated with type 2 diabetes in Hispanic elders

BACKGROUND

Hispanic elders have a high prevalence of diabetes and poor glycemic control, leading to inadequate nutritional status, muscle wasting, and impaired function.

OBJECTIVE

We examined the association of type 2 diabetes with nutritional status measured by serum albumin concentrations and midupper arm muscle area (MAM) and with function measured by difficulty with at least one activity of daily living.

DESIGN

: Health history and disability were assessed by self report in 556 Hispanics with a mean (+/- SD) age of 69 +/- 7 y and 158 non-Hispanic whites (NHW; aged 71 +/- 7 y) from the Massachusetts Hispanic Elders Survey. Energy intake (in MJ/d) and protein intake (in g/d) were estimated with use of a food-frequency questionnaire. Body mass index (BMI; in kg/m(2)) and C-reactive protein concentrations (in mg/L) were also measured. Multiple logistic regression models by ethnic group were used.

RESULTS

There were no significant differences between Hispanics and NHWs in the proportion of those with low albumin concentrations or low MAM. Hispanic diabetic women had the lowest proportion of low MAM. The risk of low serum albumin concentration was twice as high in Hispanics taking insulin as in their NHW counterparts. Among Hispanics, low albumin concentration and low BMI were associated with low MAM; female sex, low albumin concentration, high BMI, and insulin use were significantly associated with risk of functional impairment.

CONCLUSION

Type 2 diabetes is associated with poor nutritional status, muscle loss, and functional impairment among Hispanic elders.

Relation among serum and tissue concentrations of lutein and zeaxanthin and macular pigment density

BACKGROUND

Lutein and zeaxanthin are the only carotenoids in the macular region of the retina (referred to as macular pigment [MP]). Foods that are rich in lutein and zeaxanthin can increase MP density. Response to dietary lutein and zeaxanthin in other tissues has not been studied.

OBJECTIVE

The objective of this study was to examine tissue responses to dietary lutein and zeaxanthin and relations among tissues in lutein and zeaxanthin concentrations.

DESIGN

Seven subjects consumed spinach and corn, which contain lutein and zeaxanthin, with their daily diets for 15 wk. At 0, 4, 8, and 15 wk and 2 mo after the study, serum, buccal mucosa cells, and adipose tissue were analyzed for carotenoids, and MP density was measured.

RESULTS

Serum and buccal cell concentrations of lutein increased significantly from baseline during dietary modification. Serum zeaxanthin concentrations were greater than at baseline only at 4 wk, whereas buccal cell and adipose tissue concentrations of zeaxanthin did not change. Adipose tissue lutein concentrations peaked at 8 wk. Changes in adipose tissue lutein concentration were inversely related to the changes in MP density, suggesting an interaction between adipose tissue and retina in lutein metabolism. To investigate the possibility of tissue interactions, we examined cross-sectional relations among serum, tissue, and dietary lutein concentrations, anthropometric measures, and MP density in healthy adults. Significant negative correlations were found between adipose tissue lutein concentrations and MP for women, but a significant positive relation was found for men.

CONCLUSION

Sex differences in lutein metabolism may be an important factor in tissue interactions and in determining MP density.

Association of muscle power with functional status in community-dwelling elderly women

BACKGROUND

Identification of the physiologic factors most relevant to functional independence in the elderly population is critical for the design of effective interventions. It has been suggested that muscle power may be more directly related to impaired physical performance than muscle strength in elderly persons. We tested the hypothesis that peak muscle power is closely associated with self-reported functional status in sedentary elderly community-dwelling women.

METHODS

We used baseline data that were collected as part of a 1-year randomized controlled clinical trial of a combined program of strength, power, and endurance training in 80 elderly women (mean age 74.8 +/- 5.0 years) with 3.2 +/- 1.9 chronic diseases, selected for baseline functional impairment and/or falls.

RESULTS

Functional status at baseline was related in univariate analyses to physiologic capacity, habitual physical activity level, neuropsychological status, and medical diagnoses. Leg power had the strongest univariate correlation to self-reported functional status (r = -.47, p < .0001) of any of the physiologic factors we tested. In a forward stepwise regression model, leg press power and habitual physical activity level were the only two factors that contributed independently to functional status (r = .64, p < .0001), accounting for 40% of the variance in functional status.

CONCLUSIONS

Leg power is a strong predictor of self-reported functional status in elderly women.

Potential benefits of resistance exercise training on nutritional status in renal failure

Resistance or strength exercise training may help reverse the malnutrition common among patients in chronic renal failure and delay the progression of renal disease. Resistance training is characterized by resisting, lifting, and lowering weights. It results in muscle mass accretion, improved physical function, and slowed progression of muscle wasting. Resistance exercise training for a period of 8 to 12 weeks results in significant increases in muscle mass, muscle strength, and muscle function in frail "healthy" elderly individuals as well as in specific patient populations. States of malnutrition leading to muscle wasting directly affect lean tissue mass and functional capacity. Even at dietary protein intake below the Recommended Dietary Allowances, resistance training appears to exert an anabolic effect by improving energy intake and protein use allowing nitrogen retention. The potential benefits of resistance exercise extend beyond this direct impact on protein metabolism. They include improvements in functional capacity such as gait, balance, mobility, strength, exercise tolerance, improved glucose uptake, insulin sensitivity, and self-efficacy and self-esteem. Currently, the effects of resistance exercise in renal patients are unknown, although they are well shown in the case of other diseases. The potential benefits that resistance exercise training may have on muscle mass and function, nutritional status, hyperglycemia, disease progression, and the overall mental well-being of renal patients deserve further investigation. As an adjunct to current treatment modalities for chronic renal failure, resistance exercise may serve as a cost-effective, interdisciplinary, noninvasive approach to counteract malnutrition and improve the quality of life.

Conditions altering plasma concentrations of urea cycle and other amino acids in elderly human subjects

OBJECTIVE

Describe plasma amino acid concentrations and total urinary amino acid excretion in subjects from an elderly female population.

SUBJECTS

Fasting plasma samples, complete 24-hour urine samples, and 3-day diet records were obtained from 96 healthy postmenopausal women in one study and fasting plasma samples were obtained from an additional 44 subjects in 3 separate studies. In one study, nonfasting plasma samples were also collected. The subjects ranged in age from 49 to 80 years of age. Samples were obtained to allow the evaluation of the effects of fasting vs. nonfasting, normal vs. Alzheimers subjects, and level of protein intake effects.

MEASURES OF OUTCOME

Heparinized plasma samples were deproteinized with a 5-sulfosalicylic acid solution and centrifuged at 14,900 x g. Deproteinized plasma and urine samples were analyzed for free amino acids on a Beckman System 6300 analyzer using a postcolumn reaction with ninhydrin to quantitate the amino acids.

RESULTS AND CONCLUSIONS

It is concluded that: 1) From fasting plasma samples, 1 or 2 sampling days are sufficient to establish a characteristic concentration for most plasma amino acids. 2) Fasting amino acid concentrations do not reflect levels of dietary protein intake when dietary amino acid composition is similar. Shifts in fasting amino acid concentrations would be more indicative of changes in relative amounts of amino acids absorbed rather than level of dietary protein per se. 3) Totals of fasting plasma concentrations of arginine, citrulline and ornithine were relatively constant, but fluctuations occurred in the ratio of ornithine to arginine in the different populations; and 4) Patients with Alzheimers disease exhibited altered plasma ornithine and arginine concentrations relative to active or sedentary controls.

Elderly women accommodate to a low-protein diet with losses of body cell mass, muscle function, and immune response

A 9-wk study of adaptation to marginal protein intakes was conducted in 12 elderly women. Subjects were randomly assigned to two groups fed a weight-maintenance diet containing either 1.47 (low) or 2.94 (adequate) g protein.kg body cell mass-1.d-1 (0.45 and 0.92 g.kg body wt-1.d-1, respectively). Mean nitrogen balance in the low-protein group remained negative throughout the study. These subjects experienced significant losses in lean tissue, immune response, and muscle function. The adequate-protein group was in nitrogen balance throughout the study, without changes in lean tissue, and with improvements in immune response, serum immunoglobulins, albumin, total protein values, and muscle function. Thus, elderly women fed the low-protein diet accommodated to the diet by compromising functional capacity, whereas those fed the adequate diet maintained functional capacity.

Protein turnover and energy metabolism of elderly women fed a low-protein diet

The metabolic mechanisms of accommodation to a low-protein diet in elderly women were studied. Diets containing 1.47 (low) or 2.94 (adequate) g protein.kg body cell mass-1.d-1 (0.45 or 0.92 g.kg body weight-1.d-1, respectively) were fed for 10 wk. Fed state leucine kinetics, fasted and fed metabolic rate, and acute-phase responses to a bout of exercise were measured. Leucine uptake into protein, breakdown, and acute-phase responses were not significantly different within or between diet groups. In the low-protein group, leucine flux and oxidation were lower after 3 wk and oxidation continued to decrease throughout the 10-wk study. When expressed per body cell mass, metabolic rate increased over time in the low-protein group only. Leucine oxidation was a more sensitive index of the adequacy of protein intake than synthesis, flux, metabolic rate, or acute-phase response.