Prevalence and predictors of depression and suicidal ideation among adolescents attending government secondary schools in Malaysia

No abstract available.

Clinical genomics expands the morbid genome of intellectual disability and offers a high diagnostic yield

Intellectual disability (ID) is a measurable phenotypic consequence of genetic and environmental factors. In this study, we prospectively assessed the diagnostic yield of genomic tools (molecular karyotyping, multi-gene panel and exome sequencing) in a cohort of 337 ID subjects as a first-tier test and compared it with a standard clinical evaluation performed in parallel. Standard clinical evaluation suggested a diagnosis in 16% of cases (54/337) but only 70% of these (38/54) were subsequently confirmed. On the other hand, the genomic approach revealed a likely diagnosis in 58% (n=196). These included copy number variants in 14% (n=54, 15% are novel), and point mutations revealed by multi-gene panel and exome sequencing in the remaining 43% (1% were found to have Fragile-X). The identified point mutations were mostly recessive (n=117, 81%), consistent with the high consanguinity of the study cohort, but also X-linked (n=8, 6%) and de novo dominant (n=19, 13%). When applied directly on all cases with negative molecular karyotyping, the diagnostic yield of exome sequencing was 60% (77/129). Exome sequencing also identified likely pathogenic variants in three novel candidate genes (DENND5A, NEMF and DNHD1) each of which harbored independent homozygous mutations in patients with overlapping phenotypes. In addition, exome sequencing revealed de novo and recessive variants in 32 genes (MAMDC2, TUBAL3, CPNE6, KLHL24, USP2, PIP5K1A, UBE4A, TP53TG5, ATOH1, C16ORF90, SLC39A14, TRERF1, RGL1, CDH11, SYDE2, HIRA, FEZF2, PROCA1, PIANP, PLK2, QRFPR, AP3B2, NUDT2, UFC1, BTN3A2, TADA1, ARFGEF3, FAM160B1, ZMYM5, SLC45A1, ARHGAP33 and CAPS2), which we highlight as potential candidates on the basis of several lines of evidence, and one of these genes (SLC39A14) was biallelically inactivated in a potentially treatable form of hypermanganesemia and neurodegeneration. Finally, likely causal variants in previously published candidate genes were identified (ASTN1, HELZ, THOC6, WDR45B, ADRA2B and CLIP1), thus supporting their involvement in ID pathogenesis. Our results expand the morbid genome of ID and support the adoption of genomics as a first-tier test for individuals with ID.

Association between occlusal force distribution in implant overdenture prostheses and residual ridge resorption

This study aimed to investigate residual ridge resorption (RRR) of anterior and posterior maxillary and mandibular edentulous ridges, in patients treated with mandibular implant overdentures (IOD) and compare with conventional complete denture (CD) wearers, and to determine at each location, the association of RRR with the occlusal forces distribution and other patients' variables. The anterior and posterior RRR of IOD (six males, 17 females) and CD (12 males, 11 females) groups were determined using baseline and follow-up dental panaromic radiographs (DPT) (mean intervals 4 ± 1·8 years). The bone ratios were calculated using proportional area: anatomic to fixed reference areas and mean difference of ratios between the intervals determined RRR. The ridge locations included anterior and posterior maxillary and posterior mandibular arches. The T-Scan III digital occlusal system was used to record anterior and posterior percentage occlusal force (%OF) distributions. There were significant differences in anterior and posterior %OF between treatment groups. Two-way anova showed RRR was significant for arch locations (P = 0·005), treatment group (IOD versus CD) (P = 0·001), however, no significant interaction (P = 0·799). Multivariate regression analyses showed significant association between RRR and %OF at anterior maxilla (P = 0·000) and posterior mandible (P = 0·023) and for treatment groups at posterior maxilla (P = 0·033) and mandibular areas (P = 0·021). Resorption was observed in IOD compared to CD groups, with 8·5% chance of less resorption in former and 7·8% in the latter location. Depending on arch location, ridge resorption at various locations was associated with occlusal force distribution and/or treatment groups (implant prostheses or conventional complete dentures).

Abstract P6-10-04: Determining the optimal vaccination strategy using a combination of the folate binding protein (FBP) peptide vaccine (E39+GM-CSF) and an attenuated version (E39') to maximize the immunologic response in breast cancer patients

BACKGROUND FBP is overexpressed in 20-50% of breast(B) cancers(Ca) and roughly 90% of endometrial(E) and ovarian (Ov) Ca. E39 (FBP191-199, EIWTHSYKV)+GM-CSF is an HLA-A2 restricted FBP peptide vaccine, which has been shown to generate significant in vivo immunologic response(IR) in a phase I/IIa trial in E Ca and Ov Ca patients (pts). There is a risk of inducing immunologic tolerance after multiple inoculations with a highly immunogenic vaccine. Thus, we are investigating a novel vaccination series using combinations of E39 and E39' (EIWTFSTKV, an attenuated version of E39) in a phase Ib, randomized, single-center trial. We are assessing short and long-term IR. Here, we present the initial IR analysis to the primary vaccination series (PVS) within B Ca pts.

METHODS HLA-A2 positive B or Ov Ca pts were enrolled after completion of standard of care therapy and randomized into three arms: EE (6 inoculations of E39); EE'(3 inoculations of E39, then 3 of E39'); or E'E(3 of E39', then 3 of E39). Theoretically, due to lower FBP expression and less aggressive chemotherapy regimens, B Ca pts are more antigen naïve and have a less suppressed immune system. Thus, only B Ca pts were included in this analysis. The PVS includes 6 inoculations total (R1-R6), one every 3-4 weeks, and containing 250mcg GM-CSF+500mcg peptide in the first 5 pts per arm and 1000mcg of peptide in second 5 pts. To assess the in vivo IR, local reaction(LR) was measured 48 hours after each inoculation (R1-R6), and delayed type hypersensitivity(DTH) was measured pre-PVS (R0), 1, and 6-months post-PVS (RC1, RC6). Ex vivo IR was measured via dextramer assay for E39-specific CD8+ T-cells at R0, RC1, and RC6. Statistical analyses were completed using appropriate tests.

RESULTS Thirty-five B Ca pts were enrolled, with 27 completing the PVS (EE n=10, EE' n=8, E'E n=9). No clinicopathologic differences between groups or significant toxicities > grade 2 were appreciated. LR increased from R1 to R6 in all groups (ΔEE= 24.80mm, p=0.14; ΔEE'=38.13mm, p=0.07; ΔE'E=8.05mm, p=0.38), the greatest increase approaching statistical significance in the EE' arm. The only arm with a statistically significant increase for in vivo DTH from R0-RC1-RC6 was in the EE' arm (ΔEE=-6.17mm, p=0.27; ΔEE'= 44.58mm, p<0.05; ΔE'E=-1.42, p=0.37). Ex vivo analysis of IR revealed no significant difference between groups at R0(p=0.45) or RC6(p=0.72), nor within groups over time (EE p=0.32, EE' p=0.47, E'E p=0.30).

CONCLUSION In this phase Ib trial analyzing the IR of B Ca pts receiving a different vaccination strategy, both peptides were noted to be safe and immunogenic. While no difference was seen in E39-specific CD8+ T cells between groups, the in vivo response was enhanced with the use of E39' after E39; this may indicate expansion of more effective clonal populations of CD8+ T cells with this strategy. These results may be specific to B Ca pts who are relatively antigen-naïve with relatively intact immune systems. Further analysis of these pts as this trial continues will determine the optimal vaccination strategy capable of stimulating and maintaining an IR to prevent B Ca recurrence.

Citation Format: Jackson DO, Qiao N, Peace KM, Hale DF, Vreeland TJ, Greene JM, Berry JS, Trappey AF, Clifton GT, Ibrahim N, Toms A, Peoples GE, Mittendorf EA. Determining the optimal vaccination strategy using a combination of the folate binding protein (FBP) peptide vaccine (E39+GM-CSF) and an attenuated version (E39') to maximize the immunologic response in breast cancer patients [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-10-04.

Abstract PD8-05: Comparative analysis of the genomic landscape of breast cancers from women of African and European ancestry

Objectives: Paucity of data on populations of African Ancestry in clinical trials continues to limit our ability to design and implement innovative solutions to narrow the breast cancer survival gap amongst Africans, African Americans, and European Americans. We have developed a cross-continent research infrastructure to examine the spectrum of genomic alterations in breast tumors from West Africa and subsequently, to compare them to tumors from African American women and women of European Ancestry in The Cancer Genome Atlas (TCGA) database.

Methods: Consecutive women with breast cancer presenting for treatment at the University College Hospital, Ibadan and at Lagos State University Teaching Hospital, Lagos, Nigeria gave informed consent and were recruited to the West African Breast Cancer Study (WABCS) between 2013-2016. Tumor-normal pairs were subjected to exome and/or high-depth (90x) genome sequencing. High confidence somatic mutations (substitutions, insertions/deletions and structural variants) were obtained by using multiple variant callers. Furthermore, 1,089 exomic and 80 genomic breast tumor-normal pairs from TCGA were harmonized with WABCS samples, resulting in a cohort of 147 West Africans (147 exome; 40 genome), 154 African Americans (154 exome; 31 genome), and 776 Caucasians (776 exome; 43 genome).

Results: Across the exomes, genes commonly altered in breast cancer in TCGA are also altered in women of African ancestry, but the mutational spectrum is quite different, demonstrating overrepresentation of tumors with aggressive phenotypes. Overall, TP53 (65%), ERBB2 (27%), and GATA3 (17%) showed statistically significant higher alteration frequencies in West Africans and African Americans. In contrast, PIK3CA (24%) was less frequently mutated. Of note, GATA3 mutation was statistically significantly more frequent in Nigerians (39%) and African Americans (16.7%) compared to Caucasians (10.5%), in ER-positive cancers. Analysis on Structural Variants (SV), on the other hand, has shown that the genome-wide SV counts among three populations are comparable in ER-negative cancers, while Nigerians have significantly more SV counts compared to African Americans (P=0.0013) or European Americans (P=2.9x10-5) in ER-positive cancers. Similarly, genome-wide substitution patterns in ER+ and ER- cancers varied widely by race/ethnicity. In ER- cases, West Africans carried the highest proportion of canonical APOBEC-associated substitutions, particularly C>T transitions. Conversely, European Americans with ER+ disease showed a higher proportion of C>T than both West Africans (Welch t-test P = 0.044) and African Americans (Welch t-test P = 0.011). Mutation signature analyses highlighted multiple APOBEC signatures, with notable contribution differences across ancestry and ER status. A signature likely corresponding to DNA damage repair correlated with the proportion of genetic ancestry, being most prevalent in European Americans and least common in Nigerians, particularly in ER-negative cancers, with African Americans showing a degree of this signature's contribution in between the two populations (linear model adjusted for age, P=1.0x10-10).

Conclusions: Overall, our data suggests mutation spectra differences in across race/ethnicity and geography. Identification of molecular characteristics such as higher rates of HER2 enriched tumors and higher rates of GATA3 mutations in ER positive tumors are beginning to reveal the genomic basis of race-associated phenotypes and outcomes in breast cancer. Population differences in frequency and spectrum of mutations should now inform the design of innovative clinical trials that improve health equity and accelerate Precision Oncology care in diverse populations.

Citation Format: Olopade OI, Pitt JJ, Riester M, Odetunde A, Yoshimatsu T, Labrot E, Ademola A, Sanni A, Okedere B, Mahan S, Nwosu I, Leary R, Ajani M, Johnson RS, Sveen E, Zheng Y, Wang S, Fitzgerald DJ, Grundstad J, Tuteja J, Clayton W, Khramtsova G, Oludara M, Omodele F, Benson O, Adeoye A, Morhason-Bello O, Ogundiran T, Babalola C, Popoola A, Morrissey M, Chen L, Huo D, Falusi A, Winckler W, Obafunwa J, Papoutsakis D, Ojengbede O, White KP, Ibrahim N, Oluwasola O, Barretina J. Comparative analysis of the genomic landscape of breast cancers from women of African and European ancestry [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD8-05.

Drug resistance mutations among virological failure HIV-1 infected patients in Malaysia

The determination of HIV drug resistance mutations (DRMs) towards antiretroviral (ARV) drugs among HIV-1 treated patients with virological failure is crucial for further management of the patient. This study aimed to assess the most common genomic mutation and to analyse subtypes among the HIV-1 patients with viral load level > 1,000 copies/mL. A total of 101 virological failure HIV-1 patients from four different regions of Peninsular Malaysia with a viral load measurement facility were included in the study. Majority of patients (89.1%) have at least 1 mutation associated with clinical resistance to either protease inhibitors (PIs), nucleoside reverse transcriptase inhibitors (NRTIs) or nonnucleoside reverse transcriptase inhibitors (NNRTIs). Major resistance mutations among the patients towards NRTIs and NNRTIs were 70.3% and 18.8%, respectively. The most common mutation for NRTIs was M184V while K103N mutation was detected in the majority of patients who were treated with NNRTIs. The most commonly observed mutations for major PI and minor PI seen among the study population were V82A/T and L10V, respectively. In HIV-1 subtype analysis, CRF33_01B was the most predominant HIV-1 subtype in this study group. The vast detection of DRMs in this study emphasized the importance of genotypic resistance test in the management of HIV patients as DRMs can alter patient's susceptibility towards ARV drugs. Further study on larger number of samples is essential for the development of a database on HIV-1 DRMs among patients that experience virological failure in Malaysia.

Prevalence of polyoma BK virus infection among living-donor renal transplant recipients

BACKGROUND

Polyomavirus nephropathy (PVN) mainly caused by BK polyomavirus (BKPyV) remains the most common productive viral infection of the kidney in immunosuppressed patients. The diagnosis of PVN is based on the detection of BK viruria and BK viremia in conjunction with histological findings in the graft biopsy.

METHODS

Our study was aimed to estimate the prevalence of productive BKPyV infection among renal transplant patients within the first year post-transplant and identify those at risk of developing PVN. Our cross-sectional study was conducted on 134 kidney transplant patients. Evidence of BKPyV replication was assessed by viral quantification of blood and urine samples of studied patients using a quantitative real-time polymerase chain reaction (Q-PCR)PCR), detection of decoy cells in urine cytology smears, histological examination of graft biopsies from Q-PCR BKPyV-positive patients, and immunohistochemical staining by simian virus 40 (SV40) antibody.

RESULTS

Significant BKPyV infection was prevalent in 8% (n = 11) of our patients, with a peak of BKPyV infection about 8 months post transplant. BKPyV viral load by Q-PCR assay in these patients varied from 1350 to 20,000,000 (1.35 × 10(3) to 2 × 10(7) ) copies/mL for urine samples and 935 to 18,920 (9.35 × 10(2) to 1.89 × 10(4) ) copies/mL for blood samples. All the 11 patients were positive for decoy cells but only 3 developed PVN based on histology and positive SV40 staining. BKPyV infection was more prevalent in older patients. All patients responded to reduction in their immunosuppressive regimens, apart from 2 patients who required replacement of calcineurin inhibitors-based regimen with mammalian target of ramapycin inhibitors with an overall good response.

CONCLUSION

Protocol screening programs based on detection of viral replication by viruria, viremia, and decoy cells in urine are necessary to shed light on patients with high virus replication and hence increased risk of developing PVN, and to allow early diagnosis and intervention.

Dielectric Behavior of OPEFB Reinforced Polycaprolactone Composites at X-Band Frequency

Short fibres are often used as reinforcing materials with thermoplastic polymers to improve the dielectric properties of the composites. In this work, the effects of oil palm empty fruit bunch (OPEFB)-fibre loading on polycaprolactone (PCL) polymer were extensively studied. The synthesis of OPEFB-PCL composites were prepared via melt blend method. Theoretical and experimental analysis of electromagnetic (EMI) propagation, absorption and shielding effectiveness (SE) properties of the composite were also studied. The magnitudes of S-parameters for OPEFB fiber-reinforced PCL composites with different percentages of filler were measured by a rectangular waveguide connected with a microwave vector network analyzer (VNA) at (8 – 12) GHz frequency. Whilst the dielectric properties were studied using an open ended coaxial probe. The morphological characterization of the OPEFB-PCL composite was carried out using X-ray diffraction and scanning electron microscopy (SEM). This work showed that XRD profile patterns slightly changed duo to the filler loading increment which result a reduction in both dielectric constant and loss factor. However, the relative permittivity of pure oil palm fibre and PCL was measured as (1.8-j*0.08) and (2.929-j*0.3242) respectively. In addition, the composition of 12.5 wt% filler gave the highest dielectric constant and loss factor values. However, the reflection loss increases to filler content increments at the maximum frequency of 12 GHz. The excellent behavior of these polymer composites makes them superior nominees for microwave low absorption materials.

Abstract P6-03-17: Genomic landscape of breast cancers from women of African ancestry across the diaspora

Objectives: Of all ethnic/racial groups, age-standardized mortality rate from breast cancer is highest for African American women in the US for reasons that remain understudied. The paucity of genomic studies of breast tumors across the African Diaspora further restricts our understanding of the biology of breast cancer in underserved populations. To gain a better understanding of the genomic landscape of breast cancer in women of African Ancestry, we have developed a cross continent translational research infrastructure to examine the spectrum of genetic alterations in breast tumors from West Africa compared to the spectrum of alterations observed in tumors from African-American and other women who are predominantly white in The Cancer Genome Atlas (TCGA) dataset.

Methods: Peripheral blood and breast cancer biopsy tissues were collected from 214 patients enrolled in the West Africa Breast Cancer Study (WABCS) at the University of Ibadan/University College Hospital (UI/UCH) and at Lagos State University Teaching Hospital (LASUTH). Blood DNA as well as breast cancer tissue DNA and RNA were extracted at the Novartis Institutes for Biomedical Research (NIBR), UI/UCH, and LASUTH using a modified protocol of PAXgene Tissue DNA and RNA extraction method. Whole-exome (WES) and transcriptome (RNA-seq) sequencing were performed on the Illumina HiSeq2000 platform at NIBR. Single Nucleotide Variants (SNVs) and insertions/deletions (indels) were called using MuTect and Pindel, while Copy Number Alterations (CNAs) were called using an in-house implementation of the ABSOLUTE method. Observed mutations were compared against those reported in the TCGA dataset. ER, PR and HER2 status were determined by immunohistochemistry (IHC) at UI/UCH, LASUTH and UChicago.

Results: WES data for 95 tumors have been analyzed thus far. Genes commonly mutated in breast cancer in TCGA are also mutated in WABCS but the mutational spectrum is vastly different. TP53 (64%), MYC (31%), and GATA3 (26%), showed significantly higher alteration frequencies in WABCS and African Americans. In contrast, PIK3CA (20%), CDH1 (2%), and MAP3K1 (2%) were less frequently mutated in women of African ancestry. In addition to the high proportion with TP53 mutations, the proportion with HER2 positive subtype of 42.1% and triple-negative subtype of 37.9% suggest that tumors with the most aggressive features are overrepresented in breast cancer patients in West Africa.

Conclusions: In the first study of its kind, high throughput genomic analysis of the largest cohort of women of African ancestry has uncovered alterations in cancer genes, some of which may be amenable to treatment with targeted therapies. Furthermore, we provide evidence that population differences in frequency and spectrum of mutations should drive the design and deployment of precision medicine initiatives. Only then can we develop innovative interventions to reduce the unacceptably high rates of mortality from breast cancer in underserved and under resourced populations.

Citation Format: Olopade OI, Odetunde A, Riester M, Yoshimatsu T, Labrot E, Ademola A, Sanni A, Okedere B, Mahan S, Nwosu I, Leary R, Ajani M, Johnson RS, Sveen E, Zheng Y, Clayton W, Khramtsova G, Oludara M, Omodele F, Benson O, Adeoye A, Morhason-Bello O, Ogundiran T, Babalola C, Popoola A, Morrissey M, Huo D, Falusi A, Winckler W, Obafunwa J, Papoutsakis D, Ojengbede O, Ibrahim N, Oluwasola O, Barretina J. Genomic landscape of breast cancers from women of African ancestry across the diaspora. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-17.