Investigation of the Genetic Diversity and Quantitative Trait Loci Accounting for Important Agronomic and Seed Quality Traits in Brassica carinata

Brassica carinata (BBCC) is an allotetraploid in Brassicas with unique alleles for agronomic traits and has huge potential as source for biodiesel production. To investigate the genome-wide molecular diversity, population structure and linkage disequilibrium (LD) pattern in this species, we genotyped a panel of 81 accessions of B. carinata with genotyping by sequencing approach DArTseq, generating a total of 54,510 polymorphic markers. Two subpopulations were exhibited in the B. carinata accessions. The average distance of LD decay (r2 = 0.1) in B subgenome (0.25 Mb) was shorter than that of C subgenome (0.40 Mb). Genome-wide association analysis (GWAS) identified a total of seven markers significantly associated with five seed quality traits in two experiments. To further identify the quantitative trait loci (QTL) for important agronomic and seed quality traits, we phenotyped a doubled haploid (DH) mapping population derived from the "YW" cross between two parents (Y-BcDH64 and W-BcDH76) representing from the two subpopulations. The YW DH population and its parents were grown in three contrasting environments; spring (Hezheng and Xining, China), semi-winter (Wuhan, China), and spring (Wagga Wagga, Australia) across 5 years for QTL mapping. Genetic bases of phenotypic variation in seed yield and its seven related traits, and six seed quality traits were determined. A total of 282 consensus QTL accounting for these traits were identified including nine major QTL for flowering time, oleic acid, linolenic acid, pod number of main inflorescence, and seed weight. Of these, 109 and 134 QTL were specific to spring and semi-winter environment, respectively, while 39 consensus QTL were identified in both contrasting environments. Two QTL identified for linolenic acid (B3) and erucic acid (C7) were validated in the diverse lines used for GWAS. A total of 25 QTL accounting for flowering time, erucic acid, and oleic acid were aligned to the homologous QTL or candidate gene regions in the C genome of B. napus. These results would not only provide insights for genetic improvement of this species, but will also identify useful genetic variation hidden in the Cc subgenome of B. carinata to improve canola cultivars.

Abstract P6-09-24: Vitamin D level impacts odds of pathologic complete response following neoadjuvant therapy in operable breast cancer

Introduction:

Pathologic complete response (pCR) following neoadjuvant systemic chemotherapy (NAC) serves as a measure of tumor responsiveness and is a recognized surrogate for improved long-term outcomes. Some, but not all, studies have found a positive association between vitamin D (VD) and disease-free survival. We investigated if VD at diagnosis or during chemotherapy impacts pCR following neoadjuvant chemotherapy for operable breast cancer.

Methods:

Patients from Iowa were eligible if they were enrolled in one of two Iowa registries and had serum from before or during NAC tested for VD. French patients enrolled in a previous study of the impact of NAC on vitamin D and bone metabolism were considered for this study. VD deficiency was defined as <20 ng/ml. pCR was defined as no residual invasive disease in breast and lymph nodes. Firth-penalized logistic regression multivariable model was used.

Results:

The final cohort included 144 women. 84.7% of VD levels were obtained before initiation of chemotherapy. There was no difference between the French and Iowa cohorts with regard to age (p=0.20), clinical stage (p=0.22), disease receptor status (HER2+ [Hormone receptor (HR)+ or HR-], HR+/HER2-, and Triple Negative) (p=0.32) and rate of pCR (p=0.34). French women had lower body mass index (mean 24.8 vs 28.8, p<0.01), lower VD levels (mean 21.5 vs 27.5, p<0.01) and underwent lumpectomy instead of mastectomy more frequently (75.3% vs 47.8%, p<0.01) than Iowa women. Only pCR differed between the VD sufficient and deficient groups (Table 1). In multivariate analysis, after adjusting for the effects of cohort, clinical stage, and disease type by receptor status, VD deficiency put a woman at 2.68 times increased odds of not attaining a pCR (95%CI: 1.12-6.41, p=0.03) (Table 2). This variable remained significant with VD deficiency defined as <30 ng/ml and when considering this variable continuously.

Conclusion:

In this retrospective cohort, VD level before or during NAC was associated with pCR. Prospective trials could elucidate if maintaining VD levels during NAC, a highly modifiable variable, can be utilized to improve cancer outcomes in addition to benefiting other established health outcomes.

Table 1: VD Deficient and Sufficient Groups  Vitamin D (ng/ml)   Deficient (< 20)Sufficient (≥ 20)pN 5391 BMIUnderweight-Normal27 (50.9)47 (51.6)0.93 Overweight-Obese26 (49.1)44 (48.4) VD LevelBefore Chemotherapy45 (84.9)77 (84.6)0.96 During Chemotherapy8 (15.1)14 (15.4) GradeG1-224 (47.1)41 (46.1)0.91 G327 (52.9)48 (53.9) Clinical StageI-II37 (69.8)61 (67)0.73 III16 (30.2)30 (33) Receptor StatusHER2+ (HR+ or HR-)12 (22.6)29 (32.2)0.20 HR+/HER2-30 (56.6)37 (41.1)  Triple Negative11 (20.8)24 (26.7) SurgeryBreast Conserving32 (60.4)58 (63.7)0.69 Mastectomy21 (39.6)33 (36.3) pCRNo43 (81.1)53 (58.2)<.01 Yes10 (18.9)38 (41.8) AgeMean (SD)48 (10.9)51 (10.3)0.15

Table 2: Odds of Not Attaining a pCR: Multivariable Results  NOdds Ratio95% CIp-valueCohortIowa661.170.522.630.71 France77Ref   Vitamin D (<20)Deficient532.681.126.410.03 Sufficient90Ref   Clinical StageI-II97Ref    III463.251.308.110.01Receptor StatusHER2+ (HR+ or HR-)411.060.402.810.91 HR+/HER2-675.502.0414.85<0.01 Triple Negative35Ref   

Citation Format: Thomas A, Thezenas S, Mott SL, Raman R, Viala M, Pouderoux S, Schroeder MC, Lamy P-J, Jacot W. Vitamin D level impacts odds of pathologic complete response following neoadjuvant therapy in operable breast cancer [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 P6-09-24.

A Major Locus for Manganese Tolerance Maps on Chromosome A09 in a Doubled Haploid Population of Brassica napus L

Soil acidity poses a major threat to productivity of several crops; mainly due to the prevalence of toxic levels of Al³⁺ and Mn²⁺. Crop productivity could be harnessed on acid soils via the development of plant varieties tolerant to phytotoxic levels of these cations. In this study, we investigated the extent of natural variation for Mn²⁺ tolerance among ten parental lines of the Australian and International canola mapping populations. Response to Mn²⁺ toxicity was measured on the bases of cotyledon chlorosis, shoot biomass, and leaf area in nutrient solution under control (9 μM of MnCl₂⋅4H₂O) and Mn treatment (125 μM of MnCl₂⋅4H₂O). Among parental lines, we selected Darmor-bzh and Yudal that showed significant and contrasting variation in Mn²⁺ tolerance to understand genetic control and identify the quantitative trait loci (QTL) underlying Mn²⁺ tolerance. We evaluated parental lines and their doubled haploid (DH) progenies (196 lines) derived from an F₁ cross, Darmor-bzh/Yudal for Mn²⁺ tolerance. Mn²⁺-tolerant genotypes had significantly higher shoot biomass and leaf area compared to Mn²⁺-sensitive genotypes. A genetic linkage map based on 7,805 DArTseq markers corresponding to 2,094 unique loci was constructed and further utilized for QTL identification. A major locus, BnMn²⁺.A09 was further mapped with a SNP marker, Bn-A09-p29012402 (LOD score of 34.6) accounting for most of the variation in Mn²⁺ tolerance on chromosome A09. This is the first report on the genomic localization of a Mn²⁺ tolerance locus in B. napus. Additionally, an ortholog of A. thaliana encoding for cation efflux facilitator transporter was located within 3,991 bp from significant SNP marker associated with BnMn²⁺.A09. A suite of genome sequence based markers (DArTseq and Illumina Infinium SNPs) flanking the BnMn²⁺.A09 locus would provide an invaluable tool for various molecular breeding applications to improve canola production and profitability on Mn²⁺ toxic soils.

Molecular Diversity Analysis and Genetic Mapping of Pod Shatter Resistance Loci in Brassica carinata L

Seed lost due to easy pod dehiscence at maturity (pod shatter) is a major problem in several members of Brassicaceae family. We investigated the level of pod shatter resistance in Ethiopian mustard (Brassica carinata) and identified quantitative trait loci (QTL) for targeted introgression of this trait in Ethiopian mustard and its close relatives of the genus Brassica. A set of 83 accessions of B. carinata, collected from the Australian Grains Genebank, was evaluated for pod shatter resistance based on pod rupture energy (RE). In comparison to B. napus (RE = 2.16 mJ), B. carinata accessions had higher RE values (2.53 to 20.82 mJ). A genetic linkage map of an F₂ population from two contrasting B. carinata selections, BC73526 (shatter resistant with high RE) and BC73524 (shatter prone with low RE) comprising 300 individuals, was constructed using a set of 6,464 high quality DArTseq markers and subsequently used for QTL analysis. Genetic analysis of the F₂ and F_2:3 derived lines revealed five statistically significant QTL (LOD ≥ 3) that are linked with pod shatter resistance on chromosomes B1, B3, B8, and C5. Herein, we report for the first time, identification of genetic loci associated with pod shatter resistance in B. carinata. These characterized accessions would be useful in Brassica breeding programs for introgression of pod shatter resistance alleles in to elite breeding lines. Molecular markers would assist marker-assisted selection for tracing the introgression of resistant alleles. Our results suggest that the value of the germplasm collections can be harnessed through genetic and genomics tools.

Genome-wide Association Study Identifies New Loci for Resistance to Leptosphaeria maculans in Canola

Key message "We identified both quantitative and quantitative resistance loci to Leptosphaeria maculans, a fungal pathogen, causing blackleg disease in canola. Several genome-wide significant associations were detected at known and new loci for blackleg resistance. We further validated statistically significant associations in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance in canola." Blackleg, caused by Leptosphaeria maculans, is a significant disease which affects the sustainable production of canola (Brassica napus). This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to L. maculans. Genomic regions delimited with 694 significant SNP markers, that are associated with resistance evaluated using 12 single spore isolates and pathotypes from four canola stubble were identified. Several significant associations were detected at known disease resistance loci including in the vicinity of recently cloned Rlm2/LepR3 genes, and at new loci on chromosomes A01/C01, A02/C02, A03/C03, A05/C05, A06, A08, and A09. In addition, we validated statistically significant associations on A01, A07, and A10 in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance and mapped within 13.2 kb from Arabidopsis R gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of R genes of Arabidopsis thaliana and Brassica napus on the sequenced genome of B. napus cv. Darmor-bzh. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to L. maculans in canola.

Multi-environment QTL studies suggest a role for cysteine-rich protein kinase genes in quantitative resistance to blackleg disease in Brassica napus

BACKGROUND

Resistance to the blackleg disease of Brassica napus (canola/oilseed rape), caused by the hemibiotrophic fungal pathogen Leptosphaeria maculans, is determined by both race-specific resistance (R) genes and quantitative resistance loci (QTL), or adult-plant resistance (APR). While the introgression of R genes into breeding material is relatively simple, QTL are often detected sporadically, making them harder to capture in breeding programs. For the effective deployment of APR in crop varieties, resistance QTL need to have a reliable influence on phenotype in multiple environments and be well defined genetically to enable marker-assisted selection (MAS).

RESULTS

Doubled-haploid populations produced from the susceptible B. napus variety Topas and APR varieties AG-Castle and AV-Sapphire were analysed for resistance to blackleg in two locations over 3 and 4 years, respectively. Three stable QTL were detected in each population, with two loci appearing to be common to both APR varieties. Physical delineation of three QTL regions was sufficient to identify candidate defense-related genes, including a cluster of cysteine-rich receptor-like kinases contained within a 49 gene QTL interval on chromosome A01. Individual L. maculans isolates were used to define the physical intervals for the race-specific R genes Rlm3 and Rlm4 and to identify QTL common to both field studies and the cotyledon resistance response.

CONCLUSION

Through multi-environment QTL analysis we have identified and delineated four significant and stable QTL suitable for MAS of quantitative blackleg resistance in B. napus, and identified candidate genes which potentially play a role in quantitative defense responses to L. maculans.

The STRokE DOC Trial Technique: ‘Video Clip, Drip, and/or Ship’

Rationale

To describe the clinical trial methods of a site-independent telemedicine system used in stroke.

Aims

A lack of readily available stroke expertise may partly explain the low rate of rt-PA use in acute stroke. Although telemedicine systems can reliably augment expertise available to rural settings, and may increase rt-PA use, point-to-point systems do require fixed base stations. Site-independent systems may minimize delay. The STRokE DOC trial assesses whether site-independent telemedicine effectively and efficiently brings rt-PA to a remote population.

Design

STRokE DOC is a 5–year, 400–participant, noninvasive trial, comparing two consultative techniques at four remote sites. Participants are randomized to acute ‘STRokE DOC telemedicine’ or ‘telephone’ consultations. Treatment decision accuracy is adjudicated at two time points, using three levels of data availability and an independent auditor.

Study outcomes

The primary outcome measure is whether there was a ‘correct decision to treat or not to treat using rt-PA’ at each of three adjudication levels (primarily at Level #2). Secondary outcomes include the number of thrombolytic recommendations, intracerebral hemorrhage, and 90–day outcomes. Using the STRokE DOC system (or telephone evaluation), medical history, neurologic scales, CT interpretations, and recommendations have been completed on over 200 participants to date. Of the initial 11, nonrandomized, ‘run-in’ patients, six (65%) were evaluated wirelessly, and five (45%) were evaluated with a site-independent LAN or cable modem. Three (27%) received rt-PA. The adjudication methodology was able to show both agreements and disagreements in these 11 cases. It is feasible to perform site-independent stroke consultations, and adjudicate those cases, using the STRokE DOC system and trial design. Telemedicine efficacy remains to be proven.

House Dust Mites in Human ear

A study was carried out to investigate the presence of mites in human ear in 58 patients (113 ears). Ear scrapings were examined under the microscope by a parasitologist for the presence of house dust mites. Results showed the presence of house dust mites in 8 (7.1%) ears. We can conclude that mites are normal commensals of the external ears in tropical countries.

Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola

Optimum flowering time is the key to maximize canola production in order to meet global demand of vegetable oil, biodiesel and canola-meal. We reveal extensive variation in flowering time across diverse genotypes of canola under field, glasshouse and controlled environmental conditions. We conduct a genome-wide association study and identify 69 single nucleotide polymorphism (SNP) markers associated with flowering time, which are repeatedly detected across experiments. Several associated SNPs occur in clusters across the canola genome; seven of them were detected within 20 Kb regions of a priori candidate genes; FLOWERING LOCUS T, FRUITFUL, FLOWERING LOCUS C, CONSTANS, FRIGIDA, PHYTOCHROME B and an additional five SNPs were localized within 14 Kb of a previously identified quantitative trait loci for flowering time. Expression analyses showed that among FLC paralogs, BnFLC.A2 accounts for ~23% of natural variation in diverse accessions. Genome-wide association analysis for FLC expression levels mapped not only BnFLC.C2 but also other loci that contribute to variation in FLC expression. In addition to revealing the complex genetic architecture of flowering time variation, we demonstrate that the identified SNPs can be modelled to predict flowering time in diverse canola germplasm accurately and hence are suitable for genomic selection of adaptative traits in canola improvement programmes.

The prevalence and risk factors for age-related macular degeneration in rural-urban India, Sankara Nethralaya Rural-Urban Age-related Macular degeneration study, Report No. 1

PurposeTo report the age- and gender-adjusted prevalence rates of early and late age-related maculopathy (ARM) and associated risk factors in rural and urban Indian population.MethodsA population-based cross-sectional study was carried out in South India between 2009 and 2011. Of the 6617 subjects ≥60 years enumerated ones, 5495 (83.04%) participated in the eye examination. A detailed history including data on demographic, socioeconomic, and ocular history was obtained. Participants underwent detailed ophthalmic evaluation including 30° 3-field photograph as per Age-Related Eye Disease Study protocol. The ARM was graded according to the International ARM Epidemiological Study Group.ResultsAge- and gender-adjusted prevalence of early ARM was 20.91% (20.86-20.94) in the rural population and 16.37% (16.32-16.42) in the urban population. Similarly, the prevalence of late ARM was 2.26% (2.24-2.29) and 2.32% (2.29-2.34) in the rural and urban population, respectively. In both rural and urban populations, risk factors that were related to both early and late ARM were age, per year increase (OR, range 1.00-1.08); middle socioeconomic status (OR, range 1.05-1.83); and smokeless tobacco (OR, range 1.11-2.21). Protective factor in both was the presence of diabetes mellitus in all ARM (OR, range 0.34-0.83). Risk factors, only in the rural arm, were female gender (OR, range 1.06-1.64), past smoker (OR, 1.14), and serum low-density lipoprotein cholesterol level (OR, 1.03).ConclusionsThe study reports smokessless tobacco as a risk factor for both early and late ARM and identified a higher prevalence of early ARM in the rural population compared with urban population.

Abstract P1-14-14: Impact of body mass index (BMI) and neo-adjuvant chemotherapy (NAC) dosing on pathologic complete response (pCR) in operable breast cancer (bc)

Introduction:

pCR following NAC is associated with improved long term outcomes. Though obesity is associated with chemo-resistance, its impact on pCR is less clear, likely because most studies were unable to account for NAC dose adjustments. An association between taxane dose reduction and BMI has previously been shown in European populations. However, most patients (pts) with increased BMI had doses capped at BSA of 2. We studied the impact of BMI on NAC dosing when treatment is based on actual weight and whether dosing adjustments preferentially impact pCR rate.

Methods: Pts prospectively enrolled in the University of Iowa Breast Molecular Epidemiologic Resource from 2010-14 with invasive bc who received at least one cycle of NAC were eligible. Pts were stratified by BMI category: normal (BMI ≤25) or overweight-obese (BMI >25). Planned total dose was calculated based on both dosing and number of cycles. Dose reduction was defined as any decrease in total intended dose. pCR was defined as no residual invasive disease in breast and lymph nodes. To investigate the relationship between BMI, dose reductions, and pCR, chi-square tests and logistic regression models were used.

Results: 87 pts were eligible. 22 (26%), 25 (29%) and 51 (59%) of pts had HER2 positive, triple negative and hormone receptor positive bc (HER- or +), respectively. 62 (71%) pts had Stage I-II bc. All pts received a combination of taxanes with other agents (Cytoxan, 5FU, Carboplatin, Gemcitabine) with or without an anthracycline (Adriamycin or Epirubicin) or anti HER 2 therapy (Pertuzumab, Traztuzumab or Lapatinib) and were initially dosed based upon actual body weight. Taxanes were planned at treatment initiation in all pts. Anthracyclines were given to 71 (82%) pts. pCR was achieved in 28 (32%) pts. Association between BMI and NAC dosing are shown in -

Table 1: Association between NAC dosing and BMI category NormalOverweight-ObesepN3651  NoYesNoYes Taxane dose reduction30(83%)6(17%)29(57%)22(43%)<0.01Non taxane dose reduction28(78%)8(22%)40(78%)11(22%)0.94

. Relative to normal weight pts, overweight-obese pts were more likely not to achieve a pCR (OR 2.09, CI 0.84-5.21, p=0.11) and have residual disease in the breast alone (OR 2.92, CI 1.18-7.24, p=0.02). Overweight-obese pts with taxane reductions, relative to overweight-obese pts without taxane reductions, were at elevated odds of not achieving a pCR (OR 2.03, CI 0.53-7.73) -.

Table 2: Impact of taxance dose reduction on pCR by BMI category  NormalOverweight-Obese  No pCRpCRNo pCRpCRTaxane reductionNo19(63%)11(37%)20(69%)9(31%) Yes2(33%)4(67%)18(82%)4(28%)

Interaction between BMI and taxane dose reduction on pCR trended towards significance (p=0.10), a trend not seen for non-taxane drugs. The most common adverse event resulting in taxane dose reduction was neuropathy (10/28 pts).

Conclusion: Overweight-obese women experienced significantly higher rates of taxane dose reductions during NAC for bc with initial full-weight dosing. BMI status may modify the effects of taxane dose reduction on the likelihood of not achieving a pCR, Further investigation of this outcome in a larger cohort is warranted.

Citation Format: Raman R, Mott SL, Schroeder MC, Thomas A. Impact of body mass index (BMI) and neo-adjuvant chemotherapy (NAC) dosing on pathologic complete response (pCR) in operable breast cancer (bc). [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 P1-14-14.

Abstract P5-08-48: Vitamin D deficiency in various breast cancer subtypes and its impact on response to neoadjuvant chemotherapy in operable breast cancer

Introduction:

Pathologic complete response (pCR) to neoadjuvant chemotherapy (NAC) is associated with improved long-term outcomes. Vitamin D (VD) deficiency has been associated with carcinogenesis as well as poorer outcomes in breast cancer (bc) particularly in luminal-type bc. In addition, replacement of VD during adjuvant chemotherapy was found to improve disease-free survival. However, VD deficiency was not associated with pCR following NAC in one series which included patients (pts) with human epidermal growth factor receptor-2 (HER2) negative bc only. We report the relationship between VD deficiency and pCR in a cohort that includes all bc subtypes and report how VD deficiency varied by clinical and pathologic parameters.

Methods:

Patients (pts) prospectively enrolled in the University of Iowa Breast Molecular Epidemiologic Resource between 2010-14 with invasive bc, receiving at least one cycle of NAC, and who had serum collected at enrollment or during NAC were eligible. VD deficiency was defined as < 20 ng/dl. pCR was defined as no residual invasive disease in breast and lymph nodes. Patients were stratified by their BMI as normal (≤ 25 kg/m2) or overweight-obese (>25 kg/m2). To investigate the relationship between VD, clinical parameters, and NAC outcomes, chi-square, Fisher's exact, and t-tests were used.

Results:

73 pts were eligible. 52 (71%) pts had Stage I-II bc. All pts received a combination of taxanes with other agents (Cytoxan, 5FU, Carboplatin, Gemcitabine) with or without an anthracycline or anti-HER 2 therapy. 62/73 (85%) received an anthracycline. 65/73 (89%) received at least 75% of intended NAC. pCR was achieved in 25/73 (34%) pts. VD deficiency was found in 17/73 (23%) pts and was more frequent among overweight-obese pts (Table 1). VD deficiency occurred significantly more often in estrogen receptor (ER)+/progesterone receptor (PR)+/HER2- and ER+ or PR+ bc but not in HER2+ bc. Results suggest VD deficient pts may be at increased odds of not achieving a pCR (OR=3.02, p=0.10). In this cohort, VD deficient pts were at increased odds of having residual disease in the breast (OR=3.76, p=0.05), but not in the nodes (OR=1.43, p=0.53), (Table 2).

Conclusion:

Being overweight-obese was associated with VD deficiency and may warrant screening in this group. VD deficiency was significantly associated with ER+/PR+/HER2-bc and ER+ or PR+ disease. Notably, these pts are candidates for bone-injuring anti-estrogen agents as part of their overall course of therapy. VD deficiency was not significantly associated with pCR after NAC though a trend was suggested.

Table 1: VD and clinical parameters   VD Sufficient VD Deficientp  N=56N=17 Age (mean in years) 52470.16BMI≤2526(46%)3(18%)0.03 >2530(54%)14(82%) Ellis-Ellison grade1-224(43%)7(41%)0.90 332(57%)10(59%) Tumor receptorER+/PR+/HER2-15(27%)10(59%)0.02 ER+ or PR+/HER2+6(11%)3(18%)0.43 ER-/PR-/HER2+10(18%)0(0%)0.10 ER-/PR-/HER2-17(31%)3(18%)0.36 ER+ or PR+29(52%)14(82%)0.02 HER2+16(84%)3(16%)0.53

Table 2: VD and NAC Outcomes   VD SufficientVD Deficientp  N=56N=17 pCRNo34(61%)14(82%)0.10 Yes22(39%)3(18%) Breast Residual DiseaseNo25(45%)3(18%)0.05 Yes31(55%)14(84%) Node Residual DiseaseNo28(50%)7(41%)0.52 Yes28(50%)10(59%) 

Citation Format: Raman R, Link BK, Mott SL, Schroeder MC, Thomas A. Vitamin D deficiency in various breast cancer subtypes and its impact on response to neoadjuvant chemotherapy in operable breast cancer. [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 P5-08-48.

Role of folate-homocysteine pathway gene polymorphisms and nutritional cofactors in Down syndrome: A triad study

STUDY QUESTION

Do gene-gene and gene-environment interactions in folate-homocysteine (Hcy) pathway have a predisposing role for Down syndrome (DS)?

SUMMARY ANSWER

The study provides evidence that in addition to advanced age, maternal genotype, micronutrient deficiency and elevated Hcy levels, individually and in combination, are risk factors for Down syndrome.

WHAT IS KNOWN ALREADY

Polymorphisms in certain folate-Hcy-pathway genes (especially the T allele of MTHFR C677T), elevated Hcy and poor folate levels in mothers during pregnancy have been shown to be risk factors for Down syndrome in certain Asian populations (including the eastern region of India), while the same SNPs are not a risk factor in European populations. This conflicting situation alludes to differential gene-environment (nutrition) interactions in different populations which needs to be explored.

STUDY DESIGN, SIZE, DURATION

Between 2008 and 2012, 151 Down syndrome triads and 200 age-matched controls (Control mothers n = 186) were included in the study. Seven polymorphisms in six genes of folate-Hcy metabolic pathway, along with Hcy, cysteine (Cys), vitamin B12 (vit-B12) and folate levels, were analysed and compared among the case and control groups.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Genotyping was performed by the PCR-RFLP technique. Levels of homocysteine and cysteine were measured by HPLC while vitamin B12 and folate were estimated by chemiluminescence.

MAIN RESULTS AND THE ROLE OF CHANCE

We demonstrate that polymorphisms in the folate-Hcy pathway genes in mothers collectively constitute a genotypic risk for DS which is effectively modified by interactions among genes and by the environment affecting folate, Hcy and vitamin B12 levels. The study also supports the idea that these maternal risk factors provide an adaptive advantage during pregnancy supporting live birth of the DS child.

LIMITATIONS AND REASONS FOR CAUTION

Our inability to obtain genotype and nutritional assessments of unaffected siblings of the DS children was an important limitation of the study. Also, its confinement to a specific geographic region (the eastern part) of India, and relatively small sample size is a limitation. A parallel investigation on another population could add greater authenticity to the data.

WIDER IMPLICATIONS OF THE FINDINGS

For mothers genetically susceptible to deliver a DS child (particularly in South Asia), peri-conceptional nutritional supplementation and antenatal care could potentially reduce the risk of a DS child. Additionally, nutritional strategies could possibly be used for better management of the symptoms of DS children.

STUDY FUNDING/COMPETING INTERESTS

The work is funded through Programme support for Genetic disorders by Department of Biotechnology, Government of India to R.R. The authors declare no conflict of interest.

Plasmoids Formation During Simulations of Coaxial Helicity Injection in the National Spherical Torus Experiment

The formation of an elongated Sweet-Parker current sheet and a transition to plasmoid instability has for the first time been predicted by simulations in a large-scale toroidal fusion plasma in the absence of any preexisting instability. Plasmoid instability is demonstrated through resistive MHD simulations of transient coaxial helicity injection experiments in the National Spherical Torus Experiment (NSTX). Consistent with the theory, fundamental characteristics of the plasmoid instability, including fast reconnection rate, have been observed in these realistic simulations. Motivated by the simulations, experimental camera images have been revisited and suggest the existence of reconnecting plasmoids in NSTX. Global, system-size plasmoid formation observed here should also have strong implications for astrophysical reconnection, such as rapid eruptive solar events.

The discrepancy between recommendations and clinical practice for viscosupplementation in osteoarthritis: mind the gap!

Recently AAOS, ACR and OARSI revised their recommendations for the management of knee osteoarthritis (OA) and for hand, knee and hip joints. During ISIAT (International Symposium on Intra-Articular Treatments) 2013 round table on recommendations about the use of intra-articular Hyaluronic Acid (IAHA) in OA, several considerations were elaborated by the ISIAT Technical Expert Panel (TEP) regarding discrepancy between recommendations and clinical practice. The ISIAT TEP gathered the following eight suggestions regarding the drawing of recommendations on the use of IAHA in OA and its comparison with other treatments. It is necessary to merge data coming from both RCTs and registers. Only studies with a strong level of evidence should be taken into account. A common threshold of efficacy should be assessed for comparing treatments. Evaluation of hard outcomes is essential. The effect size of placebo as comparator should be attentively considered in RCTs. Particular attention should be given to different phenotypes of OA that may possibly respond differently to each treatment. Compliance and long-term side effects of different therapeutic approaches should be evaluated. Pharmacoeconomic evaluation should be performed on the long term.

Association of MDR-TB isolates with clinical characteristics of patients from Northern region of India

PURPOSE

We sought to determine the characteristics and relative frequency of transmission of MDR-TB in North India and their association with the clinical and epidemiological characteristics of TB-patients.

MATERIALS AND METHODS

To achieve the objectives PCR-SSCP, MAS-PCR and direct DNA sequencing were used against 101 Mycobacterium tuberculosis isolates.

RESULTS

Multidrug-resistant-TB isolates were found to be significantly higher (P=0.000) in previously treated patients in comparison to newly diagnosed patients. Further, significant differences (P=0.003) were observed between different age groups (Mean±SD, 28.6±11.77) of the TB patients and multidrug resistance. Most frequent mutations were observed at codons 531 and 315 of rpoB and katG genes, respectively, in MDR-TB isolates.

CONCLUSION

Routine surveillance of resistance to anti-TB drugs will improve timely recognition of MDR-TB cases and help prevent further transmission in Northern India.

Design and operation of a fast electromagnetic inductive massive gas injection valve for NSTX-U

Results from the operation of an electromagnetic valve, that does not incorporate ferromagnetic materials, are presented. Image currents induced on a conducting disc placed near a pancake solenoid cause it to move away from the solenoid and open the vacuum seal. A new and important design feature is the use of Lip Seals for the sliding piston. The pressure rise in the test chamber is measured directly using a fast time response Baratron gauge. The valve injects over 200 Torr l of nitrogen in less than 3 ms, which remains unchanged at moderate magnetic fields.

SNP markers-based map construction and genome-wide linkage analysis in Brassica napus

An Illumina Infinium array comprising 5306 single nucleotide polymorphism (SNP) markers was used to genotype 175 individuals of a doubled haploid population derived from a cross between Skipton and Ag-Spectrum, two Australian cultivars of rapeseed (Brassica napus L.). A genetic linkage map based on 613 SNP and 228 non-SNP (DArT, SSR, SRAP and candidate gene markers) covering 2514.8 cM was constructed and further utilized to identify loci associated with flowering time and resistance to blackleg, a disease caused by the fungus Leptosphaeria maculans. Comparison between genetic map positions of SNP markers and the sequenced Brassica rapa (A) and Brassica oleracea (C) genome scaffolds showed several genomic rearrangements in the B. napus genome. A major locus controlling resistance to L. maculans was identified at both seedling and adult plant stages on chromosome A07. QTL analyses revealed that up to 40.2% of genetic variation for flowering time was accounted for by loci having quantitative effects. Comparative mapping showed Arabidopsis and Brassica flowering genes such as Phytochrome A/D, Flowering Locus C and agamous-Like MADS box gene AGL1 map within marker intervals associated with flowering time in a DH population from Skipton/Ag-Spectrum. Genomic regions associated with flowering time and resistance to L. maculans had several SNP markers mapped within 10 cM. Our results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus.

A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes

Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic diversity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important amphidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 samples screened. Although the assay was designed to B. napus, successful SNP amplification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus individuals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 samples.