Correlation of the Geriatric Assessment with Overall Survival in Older Patients with Cancer

AIMS

Global guidelines recommend that all older patients with cancer receiving chemotherapy should undergo a geriatric assessment. However, utilisation of the geriatric assessment is often constrained by its time-intensive nature, which limits its adoption in settings with limited resources and high demand. There is a lack of evidence correlating the results of the geriatric assessment with survival from the Indian subcontinent. Therefore, the aims of the present study were to assess the impact of the geriatric assessment on survival in older Indian patients with cancer and to identify the factors associated with survival in these older patients.

MATERIALS AND METHODS

This was an observational study, conducted in the geriatric oncology clinic of the Tata Memorial Hospital (Mumbai, India). Patients aged 60 years and older with cancer who underwent a geriatric assessment were enrolled. We assessed the non-oncological geriatric domains of function and falls, nutrition, comorbidities, cognition, psychology, social support and medications. Patients exhibiting impairment in two or more domains were classified as frail.

RESULTS

Between June 2018 and January 2022, we enrolled 897 patients. The median age was 69 (interquartile range 65-73) years. The common malignancies were lung (40.5%), oesophagus (31.9%) and genitourinary (12.1%); 54.6% had metastatic disease. Based on the results of the geriatric assessment, 767 (85.4%) patients were frail. The estimated median overall survival in fit patients was 24.3 (95% confidence interval 18.2-not reached) months, compared with 11.2 (10.1-12.8) months in frail patients (hazard ratio 0.54; 95% confidence interval 0.41-0.72, P < 0.001). This difference in overall survival remained significant after adjusting for age, sex, primary tumour and metastatic status (hazard ratio 0.56; 95% confidence interval 0.41-0.74, P < 0.001). In the patients with a performance status of 0 or 1 (n = 454), 365 (80.4%) were frail; the median overall survival in the performance status 0-1 group was 33.0 months (95% confidence interval 24.31-not reached) in the fit group versus 14.4 months (95% confidence interval 12.25-18.73) in the frail patients (hazard ratio 0.50; 95% confidence interval 0.34-0.74, P = 0.001). In the multivariate analysis, the geriatric assessment domains that were predictive of survival were function (hazard ratio 0.68; 95% confidence interval 0.52-0.88; P = 0.003), nutrition (hazard ratio 0.64; 95% confidence interval 0.48-0.85, P = 0.002) and cognition (hazard ratio 0.67; 95% confidence interval 0.49-0.91, P = 0.011).

DISCUSSION

The geriatric assessment is a powerful prognostic tool for survival among older Indian patients with cancer. The geriatric assessment is prognostic even in the cohort of patients thought to be the fittest, i.e. performance status 0 and 1. Our study re-emphasises the critical importance of the geriatric assessment in all older patients planned for cancer-directed therapy.

Defining anthropometric thresholds (mid-arm circumference and calf circumference) in older adults residing in the community: a cross-sectional analysis using data from the population representative Longitudinal Aging Study in India (LASI DAD)

OBJECTIVES

To identify factors associated with malnutrition (undernutrition and overnutrition) and determine appropriate cut-off values for mid-arm circumference (MAC) and calf circumference (CC) among community-dwelling Indian older adults.

DESIGN

Data from the first wave of harmonised diagnostic assessment of dementia for Longitudinal Ageing Study in India (LASI-DAD) were used. Various sociodemographic factors, comorbidities, geriatric syndromes, childhood financial and health status were included. Anthropometric measurements included body mass index (BMI), MAC and CC.

SETTING

Nationally representative cohort study including 36 Indian states and union territories.

PARTICIPANTS

4096 older adults aged >60 years from LASI DAD.

OUTCOME MEASURES

The outcome variable was BMI, categorised as low (<18.5 kg/m2), normal (18.5-22.9 kg/m2) and high (>23 kg/m2). The cut-off values of MAC and CC were derived using ROC curve with BMI as the gold standard.

RESULTS

902 (weighted percentage 20.55%) had low BMI, 1742 (44.25%) had high BMI. Undernutrition was associated with age, wealth-quintile and impaired cognition, while overnutrition was associated with higher education, urban living and comorbidities such as hypertension, diabetes and chronic heart disease. For CC, the optimal lower and upper cut-offs for males were 28.1 cm and >31.5 cm, respectively, while for females, the corresponding values were 26 cm and >29 cm. Similarly, the optimal lower and upper cut-offs for MAC in males were 23.9 cm and >26.9 cm, and for females, they were 22.5 cm and >25 cm.

CONCLUSION

Our study identifies a high BMI prevalence, especially among females, individuals with higher education, urban residents and those with comorbidities. We establish gender-specific MAC and CC cut-off values with significant implications for healthcare, policy and research. Tailored interventions can address undernutrition and overnutrition in older adults, enhancing standardised nutritional assessment and well-being.

The current status of geriatric oncology in India

Geriatric oncology in India is relatively new. The number of older persons with cancer is increasing exponentially; at our institution, 34% of patients registered are 60 years and over. Apart from the Tata Memorial Hospital in Mumbai, there are currently no other Indian centers that have a dedicated geriatric oncology unit. Geriatric assessments (GAs) are done sporadically, and older patients with cancer are usually assessed and treated based on clinical judgement. Challenges to increasing the uptake of GA include a lack of training/time/interest or knowledge of the importance of the GA. Other challenges include a lack of trained personnel with expertise in geriatric oncology, and a paucity of research studies that seek to advance the outcomes in older Indian patients with cancer. We anticipate that over the next 10 years, along with the inevitable increase in the number of older persons with cancer in India, there will be a commensurate increase in the number of skilled personnel to care for them. Key goals for the future include increased research output, increased number of dedicated geriatric oncology units across the country, India-specific geriatric oncology guidelines, geriatric oncology training programs, and a focus on collaborative work across India and with global partners. In this narrative review, we provide a broad overview of the status of geriatric oncology in India, along with a description of the work done at our center. We hope to spark interest and provide inspiration to readers to consider developing geriatric oncology services in other settings.

Validation of the Onco-MPI in predicting short-term mortality in older Indian patients with cancer

INTRODUCTION

The number of older patients with cancer is increasing exponentially worldwide, and a similar trend has also been noted in India. The Multidimensional Prognostic Index (MPI) strongly correlates the presence of individual comorbidities with mortality, and the Onco-MPI prognosticates patients accurately for overall mortality. However, limited studies have evaluated this index in patient populations beyond Italy. We evaluated the performance of the Onco-MPI index in predicting mortality in older Indian patients with cancer.

MATERIALS AND METHODS

This observational study was conducted between October 2019 and November 2021 in the Geriatric Oncology Clinic at Tata Memorial Hospital in Mumbai, India. The data of patients aged ≥60 years with solid tumors who underwent a comprehensive geriatric assessment was analysed. The study's primary aim was to calculate the Onco-MPI for patients in the study and correlate it with one-year mortality.

RESULTS

A total of 576 patients aged ≥60 years were included in the study. The median age (range) of the population was 68 (60-90) years, and 429 (74.5%) were male. After a median follow-up of 19.2 months, 366 (63.7%) patients had died. The proportion of patients classified as low risk (0-0.46), moderate risk (0.47-0.63) and high risk (0.64-1.0) were 38% (219 patients), 37% (211 patients) and 25% (145 patients), respectively. There was a significant difference in one-year mortality rates between the low-risk patients compared to medium and high-risk patients (40.6% vs 53.1% vs 71.7%; p < 0.001).

DISCUSSION

The current study validates the Onco-MPI as a predictive tool for estimating short-term mortality in older Indian patients with cancer. Further prospective studies need to build on this index to obtain a score with greater discrimination in the Indian population.

The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes

Cluster bean (Cyamopsis tetragonoloba (L.) Taub 2n = 14, is commonly known as Guar. Apart from being a vegetable crop, it is an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan. Here, we are reporting a chromosome-scale reference genome assembly of a popular cluster bean cultivar RGC-936, by combining sequencing data from Illumina, 10X Genomics, Oxford Nanopore technologies. An initial assembly of 1580 scaffolds with an N50 value of 7.12 Mb was generated and these scaffolds were anchored to a high density SNP linkage map. Finally, a genome assembly of 550.31 Mb (94% of the estimated genome size of ~ 580 Mb (through flow cytometry) with 58 scaffolds was obtained, including 7 super scaffolds with a very high N50 value of 78.27 Mb. Phylogenetic analysis using single copy orthologs among 12 angiosperms showed that cluster bean shared a common ancestor with other legumes 80.6 MYA. No evidence of recent whole genome duplication event in cluster bean was found in our analysis. Further comparative transcriptomics analyses revealed pod-specific up-regulation of genes encoding enzymes involved in galactomannan biosynthesis. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted improvement of cluster bean.

Predictors of Survival Among the Oldest Old Following Acute Hospital Admission: Insights From Clinical and Biochemical Factors

Understanding the factors influencing survival in oldest old population is crucial for providing appropriate care and improving outcomes. This prospective observational study aimed to investigate the determinants of survival in acutely ill oldest old patients during acute hospitalization and 1-month follow-up. Various geriatric domains and biochemical markers were assessed. Among the 70 included patients with a median age of 87 (Inter quartile range: 85-90), the presence of diabetes, delirium, tachypnea, and high sirtuin-5 levels were associated with reduced in-hospital survival. Non-survivors had raised levels of Sirtuin 1 and Sirtuin 5, with an increase of 43% and 70%, respectively. At 1 month, delirium and diabetes were still associated with reduced survival. These findings suggest that type-2 diabetes, delirium, tachypnea, and high sirtuin-5 levels could serve as predictors of reduced survival in acutely ill, hospitalized oldest old patients.

Geriatric assessment as a predictor of survival among older Indian patients with cancer

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Background: ASCO guidelines recommend that geriatric assessment (GA) should be performed in all older adults with cancer. However, GA is labor- and time-intensive, hence the uptake is poor, especially in crowded resource poor-settings. There are no data correlating GA with overall survival (OS) outcomes from the Indian subcontinent. Methods: A prospective observational study in the geriatric oncology clinic of the Tata Memorial Hospital in Mumbai, India. Patients aged 60 years and above, with cancer who underwent a GA were enrolled. The domains assessed included: function (basic and instrumental activities of daily living, timed-up-and-go), nutrition (body mass index, unintentional weight loss, mini-nutritional assessment), comorbidities, cognition, psychological (depression, anxiety), social support, and medication (polypharmacy and potentially inappropriate medications). Patients with > 2 deranged GA domains were considered frail. Results: Between June 2018 and January 2022, 909 patients were enrolled. The median age was 69 (IQR, 60-88) years. Common malignancies included lung (40%), esophagus (21%) and head and neck (11%); 53% had metastatic disease. 80% had > 2 impaired domains in GA patients had vulnerabilities in a median of 3 (IQR, 0-5) domains. Median OS in fit patients based on the GA was 17.5 (95% CI, 13.9-21.0) months vs 12.1 (95% CI, 10.1-14.0) months in frail patients, (HR 0.66; 95% CI, 0.49-0.88, p = 0.005), which remained significant after adjusting for age, sex, and stage (HR, 0.71; 95% CI: 0.53-0.94, p = 0.021). In the multivariate analysis (Table), the domains that were predictive of survival were nutrition (HR: 0.65, 95% CI: 0.47-0.92, p = 0.014), cognition (HR: 0.65; 95% CI: 0.46-0.91, p = 0.012) and fatigue (HR: 0.74, 95% CI: 0.56-0.98, p = 0.038). Conclusions: In older Indian patients with cancer, GA is a powerful prognosticator of survival. In settings where a complete GA is not possible, nutrition, cognition, and fatigue should be the minimum domains assessed. Clinical trial information: CTRI/2020/04/024675. [Table: see text]

Prevalence and outcomes of frailty in older patients with cancer: A prospective study from geriatric oncology clinic

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Background: Frail older patients present with increased symptom burden, medical complexity and reduced tolerance to medical and surgical interventions. Data regarding the prevalence of frailty and its association with outcomes, such as overall survival, is limited from India. This study aimed to establish the prevalence of frailty and its association with overall survival (OS) in older patients with cancer. Methods: This was a prospective study conducted in geriatric oncology clinic of Tata memorial hospital (Mumbai India). Patients aged 60 years and above referred to the clinic were included. Frailty was identified using the Rockwoods Clinical frailty scale, and patients with a score of five or more were diagnosed as frail. Demographic details, type of cancer, stage and multi-domains geriatric assessment was done. Cancer and Ageing Research group online toxicity tool was used to assess the chemotherapy toxicity risk. A t-test or two-sample Wilcoxon rank-sum test was used to study the association between frailty status and non-categorical variables and the Pearson chi-squared test was used to measure the association between categorical variables. The Kaplan Meier survival estimation and the Cox proportional hazard model were used to perform the survival analysis. Results: Between June 2018 to January 2022, 909 patients were evaluated and 662 patients with clinical frailty score were included. The median age was 68 (60-86) years and 107 (16%) were above the age of 75 years. The most common malignancies were lung (39%), esophagus (21%) and head and neck (10%); 53% had metastatic disease. 192 (29%) were frail, and it prevalence increased with age. Frailty status was associated with poor OS (unadjusted HR: 2.512; 95% CI: 1.931-3.268). This association was significant even after adjusting for age, gender, BMI and stage of cancer (adjusted HR: 2.104; 95% CI: 1.598-2.770). Frailty was associated with comorbidities such as diabetes (32% vs 23%, p = 0.014), chronic obstructive pulmonary disease (13% vs 7%, p = 0.045) and cardiovascular disease (19% vs 12%, p = 0.017). Among the geriatric domains, frail patients had greater incidence of polypharmacy (52% vs 33%, p < 0.01), slower gait speed (53% vs 12%, p < 0.01), impaired cognition (25% vs 7%, p < 0.01), poor nutritional status (51% vs 17%, p < 0.001), depression (29% vs 8%, p < 0.01) and anxiety (14% vs 5%, p < 0.01). Conclusions: The prevalence of frailty among older cancer patients is high. It is associated with poor physical, cognitive and psychological resilience and is associated with poor overall survival. Our study supports the routine assessment of frailty in older patients with cancer to guide treatment decisions. Clinical trial information: CTRI/2020/04/024675.

Addressing the Needs of Older Adults With Cancer in Low- and Middle-Income Settings

The number of older adults in the world is projected to increase steeply over the next 30 years; most older adults will live in low- and middle-income countries. This will have a direct impact on the global cancer burden, as cancer is largely a disease of aging. A revolution in the way we care for older adults in low- and middle-income settings is needed to meet rapidly rising demands. Regardless of a nation's relative wealth or resources, implementing the geriatric assessment in cancer care has presented a challenge because of omission of the principles of geriatric oncology from formal training and continuing education, lack of time, and a shortage of qualified personnel. To meet the challenge of caring for older adults globally, we must: (1) re-imagine aging-focused training for providers and nurses, (2) create and strengthen collaborations/partnerships between geriatric oncology teams and aging-service organizations, and (3) increase advocacy for age-friendly health care policy. By harnessing technology, the reach of specialized oncology education and care can be extended even-or especially-to low- and middle-income settings.

Parkinsonism: An emerging post COVID sequelae

Parkinsonism has a complex and multifactorial aetiology and the role of post viral infection parkinsonism has been documented. The recent pandemic has made it clear that COVID-19 causes respiratory disease and affects multiple organs, which includes the central nervous system. Here we report three cases of post COVID parkinsonism occurring in older adults, age 60 years and above, and their response to levodopa-carbidopa.

Xanthogranulomatous pyelonephritis due to Aspergillus in a non-diabetic older patient

Xanthogranulomatous pyelonephritis is a rare condition characterised by destructive granulomatous inflammation of renal parenchyma. Primary renal Aspergillosis has been reported in patients with immunocompromised states such as diabetes, retroviral disease, organ transplant recipients, etc. We present a unique case of an older adult in his early 60s, presenting with fever and left flank pain with renal angle tenderness, diagnosed with primary renal aspergillosis with xanthogranulomatous pyelonephritis. These symptoms resolved with a long duration of antifungal (itraconazole) therapy and nephrectomy. The unique features are the development of fungal pyelonephritis in the absence of any immunocompromising conditions and the development of xanthogranulomatous changes with no risk factors.

Chemotactic factor inducing Interleukin-8 (IL8) gene is transcriptionally elevated in experimental enterotoxaemia in goats caused by Clostridium perfringens type D

The current study was designed to analyse the effects of experimental induction of enterotoxaemia through intra-duodenal inoculation of C. perfringens type D culture isolated from spontaneous outbreaks in goats. Twenty goats (6–9 month age) were divided into four groups and C. perfringens type D culture was inoculated intra-duodenally as per following: Group-I (whole cultures-WC), group-II (culture supernatant-CS), group-III (washed cells-WS), and group-IV (uninfected control-C). The treated animals were sacrificed after 72 h post infection (hpi), and necropsy showed gross changes including haemorrhages and congestion in the ileal and colon mucosa, pulmonary congestion and edema in lung. Kidney, brain and spleen exhibited severe to moderate congestion. Microscopic changes like haemorrhages, degenerative and necrotic changes in the mucosal epithelium of intestine and haemorrhages in kidney parenchyma were observed in the H&E stained sections. Lung alveolar sacs were filled with proteinaceous fluid. Immunohistochemistry revealed positive immunolabelling for etx (epsilon toxin) in the mucosa of intestine in WC and CS group. Control animals did not exhibit any significant gross or microscopic changes. PCR amplification of DNA extracted from intestinal tissues of WC and CS groups showed positive for etx gene demonstrating the production of epsilon toxin. Transcriptional responses in experimental groups were assessed by quantitative reverse transcription real time PCR (qRT-PCR). Genes including IL-1β and IL2 showed up-regulation in all the experimental groups (WC, CS&WS). Specifically the toxin-based experimental groups (WC&CS) showed up-regulation of the gene responsible for chemotaxis viz. IL-8, while the washed cells group (WS) showed higher transcriptional response to Cathepsin-L (Cat-L) gene denoting the acute inflammatory response due to neutrophil elastase activity. These results take a cue on the evolving nature of the enterotoxaemia in goats due to various strains circulating in the field. The host response and its modulation due to the novel enterotoxaemia strains throws light on the current challenges in efficient control of the disease in goats.

Case Report: Hypercalcemia in an Older Patient with Type I Lepra Reaction

Leprosy is a rare, chronic granulomatous disease, and India accounts for two-thirds of the new cases reported worldwide. Hypercalcemia is a rare complication of granulomatous disease. Here, we report a case of an older adult patient with leprosy and type I lepra reaction presenting with severe hypercalcemia.

Behavioural issues in late life may be the precursor of dementia- A cross sectional evidence from memory clinic of AIIMS, India

Background

Mild Behavioural Impairment (MBI), an “at risk” state for incident cognitive declin, is characterized by late onset, sustained neuropsychiatric symptoms of any severity which cannot be accounted for by other formal medical and psychiatric nosology. There is no study related to MBI from India.

Methods and findings

In this cross-sectional observational study 124 subjects 60 years and above were recruited between March 2017 to October 2018, from memory clinic of department of Geriatric medicine with memory or behavioural complains. Subjects with major neurocognitive impairment (CDR score of 1 or more), major depressive disorder, generalized anxiety disorder and impaired activities of daily living (ADL) were excluded. Subjects with Mild Cognitive impairment (MCI) (CDR- 0.5), and Subjective cognitive impairment (SCI) (CDR- 0) were included. Neuropsychiatric Inventory Questionnaire (NPI-Q) was used to identify the presence of NPS. The ISTAART-MBI (International Society of Advance Alzheimer’s Research and Treatment-Alzheimer’s Association) diagnostic criteria was used to diagnose MBI. All the participants underwent a geriatric assessment using standardised screening. The objectives of this study was to determine the frequency of mild behavioural impairment (MBI), and its domains, in MCI or SCI and its association with comorbidities and geriatric syndromes. The mean age of the participants was 69.21, 71.77% (89) were male and 28.23% (35) were female. 41.13% (51) of these individuals were diagnosed with MBI. The MBI and non MBI group differed significantly in marital status, cognitive status and MCI subtype. The proportion of domains involved are as follows: decreased motivation 60.78%(31), emotional dysregulation 54.90% (28), impulse dyscontrol 68.63% (35), social inappropriateness 21.57%(11), abnormal perception 2 (3.93%). Presence of multi-morbidity, and diabetes, were statistically significant between the groups.

Conclusion

This study presents the first clinic-based prevalence estimates of MBI from Asia. Findings indicate a relatively high prevalence of MBI in predementia clinical states, impulse dyscontrol was the most commonly involved MBI domain. Multimorbidity, diabetes, urinary incontinence were other determinants of MBI.

Identification and characterization of trait-specific SNPs using ddRAD sequencing in water buffalo

Single Nucleotide Polymorphism (SNP) is one of the important molecular markers widely used in animal breeding program for improvement of any desirable genetic traits. Considering this, the present study was carried out to identify, annotate and analyze the SNPs related to four important traits of buffalo viz. milk volume, age at first calving, post-partum cyclicity and feed conversion efficiency. We identified 246,495, 168,202, 74,136 and 194,747 genome-wide SNPs related to mentioned traits, respectively using ddRAD sequencing technique based on 85 samples of Murrah Buffaloes. Distribution of these SNPs were highest (61.69%) and lowest (1.78%) in intron and exon regions, respectively. Under coding regions, the SNPs for the four traits were further classified as synonymous (4697) and non-synonymous (3827). Moreover, Gene Ontology (GO) terms of identified genes assigned to various traits. These characterized SNPs will enhance the knowledge of cellular mechanism for enhancing productivity of water buffalo through molecular breeding.

Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat

The genetics of coat color variation remains a classic area. Earlier studies have focused on a limited number of genes involved in color determination; however, the complete set of trait determinants are still not well known. In this study, we used high-throughput sequencing technology to identify and characterize intricate interactions between genes that cause complex coat color variation in Changthangi Pashmina goats, producer of finest and costly commercial animal fiber. We systematically identified differentially expressed mRNAs and lncRNAs from black, brown and white Pashmina goat skin samples by using RNA-sequencing technique. A pairwise comparison of black, white and brown skin samples yielded 2479 significantly dysregulated genes (2422 mRNA and 57 lncRNAs). Differentially expressed genes were enriched in melanin biosynthesis, melanocyte differentiation, developmental pigmentation, melanosome transport activities GO terms. Our analysis suggested the potential role of lncRNAs on color coding mRNAs in cis and trans configuration. We have also developed online data repository as a component of the study to provide a central location for data access, visualization and interpretation accessible through http://pcd.skuastk.org/.

Unravelling the epigenomic interactions between parental inbreds resulting in an altered hybrid methylome in pigeonpea

DNA methylation is an important heritable landmark conferring epigenetic changes in hybrids and has fascinated biologists and plant-breeders over the years. Although epigenetic changes have been documented in rice and maize hybrids, such investigations have not been reported in pigeonpea. Here, we report genome-wide methylation profiles of pigeonpea sterile and fertile inbred lines and their fertile F1 hybrid at single base resolution. We found that pigeonpea genome is relatively enriched in CG methylation. Identification of differentially methylated regions (DMRs) in the sterile and fertile parent revealed remarkable differences between their methylation patterns. Investigation of methylation status of parental DMRs in hybrid revealed non-additive methylation patterns resulting from trans-chromosomal methylation and trans-chromosomal demethylation events. Furthermore, we discovered several DMRs negatively associated with gene expression in the hybrid and fertile parent. Interestingly, many of those DMRs belonged to transposable elements and genes encoding pentatricopeptide repeats associated proteins, which may mediate a role in modulating the genes impacting pollen fertility. Overall, our findings provide an understanding of two parental epigenomes interacting to give rise to an altered methylome in pigeonpea hybrids, from genome-wide point of view.

The complete mitochondrial genome of the Asian stinging catfish, Heteropneustes fossilis (Siluriformes, Heteropneustidae) and its comparison with other related fish species

The complete mitogenome of Heteropneustes fossilis is described using Ion Torrent (PGM sequencer), which showed it was 16,489 bp in size comprising 13 mRNAs, 22 tRNAs, 2 rRNA genes, and 858 bp as D-Loop control region, along with gene order and organization, being similar to most of the other related Siluriformes fish mitogenome of NCBI databases. The 20 RNAs were packed into a typical cloverleaf structure. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of H. fossilis mitogenome reported earlier and also would be helpful in understanding the population genetics, phylogenetics, and evolution of catfishes.

A computational approach for prediction of donor splice sites with improved accuracy

Identification of splice sites is important due to their key role in predicting the exon-intron structure of protein coding genes. Though several approaches have been developed for the prediction of splice sites, further improvement in the prediction accuracy will help predict gene structure more accurately. This paper presents a computational approach for prediction of donor splice sites with higher accuracy. In this approach, true and false splice sites were first encoded into numeric vectors and then used as input in artificial neural network (ANN), support vector machine (SVM) and random forest (RF) for prediction. ANN and SVM were found to perform equally and better than RF, while tested on HS3D and NN269 datasets. Further, the performance of ANN, SVM and RF were analyzed by using an independent test set of 50 genes and found that the prediction accuracy of ANN was higher than that of SVM and RF. All the predictors achieved higher accuracy while compared with the existing methods like NNsplice, MEM, MDD, WMM, MM1, FSPLICE, GeneID and ASSP, using the independent test set. We have also developed an online prediction server (PreDOSS) available at http://cabgrid.res.in:8080/predoss, for prediction of donor splice sites using the proposed approach.

Identification of species based on DNA barcode using k-mer feature vector and Random forest classifier

DNA barcoding is a molecular diagnostic method that allows automated and accurate identification of species based on a short and standardized fragment of DNA. To this end, an attempt has been made in this study to develop a computational approach for identifying the species by comparing its barcode with the barcode sequence of known species present in the reference library. Each barcode sequence was first mapped onto a numeric feature vector based on k-mer frequencies and then Random forest methodology was employed on the transformed dataset for species identification. The proposed approach outperformed similarity-based, tree-based, diagnostic-based approaches and found comparable with existing supervised learning based approaches in terms of species identification success rate, while compared using real and simulated datasets. Based on the proposed approach, an online web interface SPIDBAR has also been developed and made freely available at http://cabgrid.res.in:8080/spidbar/ for species identification by the taxonomists.

Mapping QTLs for Salt Tolerance in Rice (Oryza sativa L.) by Bulked Segregant Analysis of Recombinant Inbred Lines Using 50K SNP Chip

Soil salinity is a major constraint to rice production in large inland and coastal areas around the world. Modern high yielding rice varieties are particularly sensitive to high salt stress. There are salt tolerant landraces and traditional varieties of rice but with limited information on genomic regions (QTLs) and genes responsible for their tolerance. Here we describe a method for rapid identification of QTLs for reproductive stage salt tolerance in rice using bulked segregant analysis (BSA) of bi-parental recombinant inbred lines (RIL). The number of RILs required for the creation of two bulks with extreme phenotypes was optimized to be thirty each. The parents and bulks were genotyped using a 50K SNP chip to identify genomic regions showing homogeneity for contrasting alleles of polymorphic SNPs in the two bulks. The method was applied to ‘CSR11/MI48’ RILs segregating for reproductive stage salt tolerance. Genotyping of the parents and RIL bulks, made on the basis of salt sensitivity index for grain yield, revealed 6,068 polymorphic SNPs and 21 QTL regions showing homogeneity of contrasting alleles in the two bulks. The method was validated further with ‘CSR27/MI48’ RILs used earlier for mapping salt tolerance QTLs using low-density SSR markers. BSA with 50K SNP chip revealed 5,021 polymorphic loci and 34 QTL regions. This not only confirmed the location of previously mapped QTLs but also identified several new QTLs, and provided a rapid way to scan the whole genome for mapping QTLs for complex agronomic traits in rice.