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Article ; Online: Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA.

Gong, Binsheng / Lababidi, Samir / Kusko, Rebecca / Bouri, Khaled / Prezek, Sarah / Thovarai, Vishal / Prasanna, Anish / Maier, Ezekiel J / Golkaram, Mahdi / Sun, Xingqiang / Kyriakidis, Konstantinos / Kitajima, João Paulo / Ebrahim Sahraeian, Sayed Mohammad / Guo, Yunfei / Johanson, Elaine / Jones, Wendell / Tong, Weida / Xu, Joshua

Scientific reports

2024 Volume 14, Issue 1, Page(s) 8165

Abstract: Accurately calling indels with next-generation sequencing (NGS) data is critical for clinical application. The precisionFDA team collaborated with the U.S. Food and Drug Administration's (FDA's) National Center for Toxicological Research (NCTR) and ... ...

Abstract	Accurately calling indels with next-generation sequencing (NGS) data is critical for clinical application. The precisionFDA team collaborated with the U.S. Food and Drug Administration's (FDA's) National Center for Toxicological Research (NCTR) and successfully completed the NCTR Indel Calling from Oncopanel Sequencing Data Challenge, to evaluate the performance of indel calling pipelines. Top performers were selected based on precision, recall, and F1-score. The performance of many other pipelines was close to the top performers, which produced a top cluster of performers. The performance was significantly higher in high confidence regions and coding regions, and significantly lower in low complexity regions. Oncopanel capture and other issues may have occurred that affected the recall rate. Indels with higher variant allele frequency (VAF) may generally be called with higher confidence. Many of the indel calling pipelines had good performance. Some of them performed generally well across all three oncopanels, while others were better for a specific oncopanel. The performance of indel calling can further be improved by restricting the calls within high confidence intervals (HCIs) and coding regions, and by excluding low complexity regions (LCR) regions. Certain VAF cut-offs could be applied according to the applications.
MeSH term(s)	INDEL Mutation ; High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2024-04-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-58573-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Synthetic Health Data Can Augment Community Research Efforts to Better Inform the Public During Emerging Pandemics.

Prasanna, Anish / Jing, Bocheng / Plopper, George / Miller, Kristina Krasnov / Sanjak, Jaleal / Feng, Alice / Prezek, Sarah / Vidyaprakash, Eshaw / Thovarai, Vishal / Maier, Ezekiel J / Bhattacharya, Avik / Naaman, Lama / Stephens, Holly / Watford, Sean / Boscardin, W John / Johanson, Elaine / Lienau, Amanda

medRxiv : the preprint server for health sciences

2023

Abstract: The COVID-19 pandemic had disproportionate effects on the Veteran population due to the increased prevalence of medical and environmental risk factors. Synthetic electronic health record (EHR) data can help meet the acute need for Veteran population- ... ...

Abstract	The COVID-19 pandemic had disproportionate effects on the Veteran population due to the increased prevalence of medical and environmental risk factors. Synthetic electronic health record (EHR) data can help meet the acute need for Veteran population-specific predictive modeling efforts by avoiding the strict barriers to access, currently present within Veteran Health Administration (VHA) datasets. The U.S. Food and Drug Administration (FDA) and the VHA launched the precisionFDA COVID-19 Risk Factor Modeling Challenge to develop COVID-19 diagnostic and prognostic models; identify Veteran population-specific risk factors; and test the usefulness of synthetic data as a substitute for real data. The use of synthetic data boosted challenge participation by providing a dataset that was accessible to all competitors. Models trained on synthetic data showed similar but systematically inflated model performance metrics to those trained on real data. The important risk factors identified in the synthetic data largely overlapped with those identified from the real data, and both sets of risk factors were validated in the literature. Tradeoffs exist between synthetic data generation approaches based on whether a real EHR dataset is required as input. Synthetic data generated directly from real EHR input will more closely align with the characteristics of the relevant cohort. This work shows that synthetic EHR data will have practical value to the Veterans' health research community for the foreseeable future.
Language	English
Publishing date	2023-12-13
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.11.23298687
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Article ; Online: An observer-blinded, cluster randomised trial of a typhoid conjugate vaccine in an urban South Indian cohort.

Sahai, Nikhil / Arunachalam, Dilesh Kumar / Morris, Tim / Copas, Andrew / Samuel, Prasanna / Mohan, Venkata Raghava / Abraham, Vinod / Selwyn, Joshua Anish / Kumar, Praveen / Rose, Winsley / Balaji, Veeraraghavan / Kang, Gagandeep / John, Jacob

Trials

2023 Volume 24, Issue 1, Page(s) 492

Abstract: Background: Typhoid fever causes nearly 110,000 deaths among 9.24 million cases globally and disproportionately affects developing countries. As a control measure in such regions, typhoid conjugate vaccines (TCVs) are recommended by the World Health ... ...

Abstract	Background: Typhoid fever causes nearly 110,000 deaths among 9.24 million cases globally and disproportionately affects developing countries. As a control measure in such regions, typhoid conjugate vaccines (TCVs) are recommended by the World Health Organization (WHO). We present here the protocol of a cluster randomised vaccine trial to assess the impact of introducing TyphiBEV® vaccine to those between 1 and 30 years of age in a high-burden setting. Methods: The primary objective is to determine the relative and absolute rate reduction of symptomatic, blood-culture-confirmed S. Typhi infection among participants vaccinated with TyphiBEV® in vaccine clusters compared with the unvaccinated participants in non-vaccine clusters. The study population is residents of 30 wards of Vellore (a South Indian city) with participants between the ages of 1 and 30 years who provide informed consent. The wards will be divided into 60 contiguous clusters and 30 will be randomly selected for its participants to receive TyphiBEV® at the start of the study. No placebo/control is planned for the non-intervention clusters, which will receive the vaccine at the end of the trial. Participants will not be blinded to their intervention. Episodes of typhoid fever among participants will be captured via stimulated, passive fever surveillance in the area for 2 years after vaccination, which will include the most utilised healthcare facilities. Observers blinded to the participants' intervention statuses will record illness details. Relative and absolute rate reductions will be calculated at the end of this surveillance and used to estimate vaccine effectiveness. Discussion: The results from our trial will allow countries to make better-informed decisions regarding the TCV that they will roll-out and may improve the global supplies and affordability of the vaccines. Trial registration: Clinical Trials Registry of India (CTRI) CTRI/2022/03/041314. Prospectively registered on 23 March 2022 ( https://ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=62548&EncHid=&userName=vellore%20typhoid ). CTRI collects the full WHO Trial Registration Data Set.
MeSH term(s)	Humans ; Infant ; Child, Preschool ; Child ; Adolescent ; Young Adult ; Adult ; Typhoid Fever/epidemiology ; Typhoid Fever/prevention & control ; Vaccines, Conjugate ; Typhoid-Paratyphoid Vaccines/adverse effects ; Vaccination ; India
Chemical Substances	Vaccines, Conjugate ; Typhoid-Paratyphoid Vaccines
Language	English
Publishing date	2023-08-03
Publishing country	England
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	2040523-6
ISSN	1745-6215 ; 1468-6694 ; 1745-6215
ISSN (online)	1745-6215
ISSN	1468-6694 ; 1745-6215
DOI	10.1186/s13063-023-07555-y
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Article: Radiofrequency ablation using Barrx

Patel, Anish / Patel, Sunil / Wickremesinghe, Prasanna C / Vadada, Deepak

Clinical and experimental gastroenterology

2017 Volume 10, Page(s) 113–120

Abstract: Gastric antral vascular ectasia (GAVE), also known as "watermelon stomach", is an uncommon condition, which can cause gastrointestinal bleeding due to rupture of blood vessels that line the stomach. The pathogenesis of GAVE remains unclear; however it is ...

Abstract	Gastric antral vascular ectasia (GAVE), also known as "watermelon stomach", is an uncommon condition, which can cause gastrointestinal bleeding due to rupture of blood vessels that line the stomach. The pathogenesis of GAVE remains unclear; however it is thought that hemodynamic changes, mechanical stress, and autoimmune factors all have a part to play. A range of conditions are also commonly associated with the syndrome, such as portal hypertensive gastropathy, liver cirrhosis, and autoimmune disorders. Less commonly, chronic renal failure, cardiac diseases, and bone marrow transplantation have coexisted with GAVE. The diagnosis is usually based on visualization of the tissue upon endoscopy; however, histology plays a role in uncertain cases. The typical "watermelon" appearance relates to the tissue having a striped appearance radiating out from the pylorus. Medical treatment has failed to show satisfactory results and surgery is usually considered as a last resort, due to its increased risk for complications and mortality. Lasers and argon plasma coagulation have been used recently, and been shown to be as effective as surgery and a safer option. We present three cases of gastric antral vascular ectasia treated at our institution with radiofrequency ablation and review the literature on treatment modalities for GAVE.
Language	English
Publishing date	2017-07-10
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2520690-4
ISSN	1178-7023
ISSN	1178-7023
DOI	10.2147/CEG.S80241
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Article: The seroprevalence of immunoglobulin A transglutaminase in type 1 diabetic patients of South Indian origin.

Pulikkal, Annie A / Kolly, Anish / Prasanna Kumar, K M / Shivaprasad, C

Indian journal of endocrinology and metabolism

2016 Volume 20, Issue 2, Page(s) 233–237

Abstract: Context: Celiac disease (CD) is a commonly encountered autoimmune condition in patients with type 1 diabetes (T1D). There is sparse data on the seroprevalence of immunoglobulin A (IgA) transglutaminase (tTG) in T1D patients of South Indian origin.: ... ...

Abstract	Context: Celiac disease (CD) is a commonly encountered autoimmune condition in patients with type 1 diabetes (T1D). There is sparse data on the seroprevalence of immunoglobulin A (IgA) transglutaminase (tTG) in T1D patients of South Indian origin. Aims: To detect the prevalence of IgA tTG in T1D patients of South Indian origin. To evaluate the relation between the presence of autoimmunity and metabolic control and complications of diabetes. Materials and methods: We conducted a cross-sectional study on 258 T1D patients. All the patients were subjected to biochemical tests and evaluated for microvascular complications. IgA tTG was estimated by ELISA. IgA tTG levels >40 AU/ml was considered positive. Results: Of the 258 participants, 12 (4.65%) were found to be positive for IgA tTG antibodies. Distribution of IgA positivity was equal in both sexes. There was a significant negative correlation of IgA tTG positivity with hemoglobin and glycated hemoglobin (HbA1c). Conclusions: The seropositivity of CD in South Indian patients with T1D has been observed to be 4.68%. This is much lower compared to studies from North India. This can be explained by both the genetic and dietary factors. The seropositivity correlated negatively with hemoglobin and HbA1c.
Language	English
Publishing date	2016-01-31
Publishing country	India
Document type	Journal Article
ZDB-ID	2600211-5
ISSN	2230-9500 ; 2230-8210
ISSN (online)	2230-9500
ISSN	2230-8210
DOI	10.4103/2230-8210.176359
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Article ; Online: MicroRNA expression patterns in HbE/β-thalassemia patients: The passwords to unlock fetal hemoglobin expression in β-hemoglobinopathies.

Das, Sankha Subhra / Das, Subhayan / Byram, Prasanna Kumar / Rahaman, Motiur / Dolai, Tuphan Kanti / Chatterjee, Anish / Chakravorty, Nishant

Blood cells, molecules & diseases

2020 Volume 87, Page(s) 102523

Abstract: Hemoglobin E (HbE)/β-thalassemia is a form of β-hemoglobinopathy that is well-known for its clinical heterogeneity. Individuals suffering from this condition are often found to exhibit increased fetal hemoglobin (HbF) levels - a factor that may ... ...

Abstract	Hemoglobin E (HbE)/β-thalassemia is a form of β-hemoglobinopathy that is well-known for its clinical heterogeneity. Individuals suffering from this condition are often found to exhibit increased fetal hemoglobin (HbF) levels - a factor that may contribute to their reduced blood transfusion requirements. This study hypothesized that the high HbF levels in HbE/β-thalassemia individuals may be guided by microRNAs and explored their involvement in the disease pathophysiology. The miRNA expression profile of hematopoietic progenitor cells in HbE/β-thalassemia patients was investigated and compared with that of healthy controls. Using miRNA PCR array experiments, eight miRNAs (hsa-miR-146a-5p, hsa-miR-146b-5p, hsa-miR-148b-3p, hsa-miR-155-5p, hsa-miR-192-5p, hsa-miR-335-5p, hsa-miR-7-5p, hsa-miR-98-5p) were identified to be significantly up-regulated whereas four miRNAs (hsa-let-7a-5p, hsa-miR-320a, hsa-let-7b-5p, hsa-miR-92a-3p) were significantly down-regulated. Target analysis found them to be associated with several biological processes and molecular functions including MAPK and HIF-1 signaling pathways - the pathways known to be associated with HbF upregulation. Results of dysregulated miRNAs further indicated that miR-17/92 cluster might be of critical importance in HbF regulation. The findings of our study thus identify key miRNAs that can be extrinsically manipulated to elevate HbF levels in β-hemoglobinopathies.
MeSH term(s)	Cells, Cultured ; Down-Regulation ; Fetal Hemoglobin/genetics ; Gene Expression Profiling ; Gene Regulatory Networks ; Hemoglobin E/genetics ; Humans ; MicroRNAs/genetics ; Transcriptome ; Up-Regulation ; beta-Thalassemia/genetics
Chemical Substances	MicroRNAs ; Hemoglobin E (9034-61-1) ; Fetal Hemoglobin (9034-63-3)
Language	English
Publishing date	2020-11-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1237083-6
ISSN	1096-0961 ; 1079-9796
ISSN (online)	1096-0961
ISSN	1079-9796
DOI	10.1016/j.bcmd.2020.102523
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Article ; Online: High prevalence of organ specific autoantibodies in Indian type 1 diabetic patients.

Shivaprasad, Channabasappa / Kolly, Anish / Pulikkal, Annie / Kumar, K M Prasanna

Journal of pediatric endocrinology & metabolism : JPEM

2017 Volume 30, Issue 7, Page(s) 707–712

Abstract: Background: Type 1 diabetes (T1D) is frequently associated with other autoimmune conditions such as autoimmune thyroiditis, coeliac disease (CD) and Addison's disease. There are sparse data on the prevalence of antibodies against these conditions in ... ...

Abstract	Background: Type 1 diabetes (T1D) is frequently associated with other autoimmune conditions such as autoimmune thyroiditis, coeliac disease (CD) and Addison's disease. There are sparse data on the prevalence of antibodies against these conditions in Indian patients with T1D. This study aims to evaluate prevalence of these T1D associated autoantibodies in Indian patients. Methods: Two hundred and fifty-eight patients with T1D were recruited from the Bangalore Diabetes Hospital and the Vydehi Institute of Medical Sciences and Research Centre (VIMS) for the study. Participants diagnosed with diabetes before the age of 18 years, as per the American Diabetes Association (ADA) criteria, and who were classified as T1D based on clinical grounds were recruited for the study. Anti-thyroid peroxidase antibody (TPO) and IgA tissue transglutaminase antibody (tTG) were estimated in all the patients. 21-Hydroxylase antibody (21-OHAb) were estimated in 170 patients. All assays were done by commercial immunoassay. Eighty-eight unrelated age-matched healthy controls were chosen for comparison. Results: The mean age of T1D patients was 14.33 years. The mean duration of diabetes was 4.88 years. Anti-TPO was positive in 43 (16.7%) patients with T1D as compared to 3 (3.4%) in controls. IgA tTG was positive in 12 (4.65%) patients with T1D and was absent in controls. 21-OHAb was positive in two (1.1%) patients with T1D and was absent in controls. Both patients who had positive 21-OHab had the other two antibodies. Five patients had positive anti-TPO and IgA-tTG antibodies. Conclusions: Anti-TPO antibody was the most prevalent antibody in patients with T1D. Anti-TPO and IgA-tTG antibodies were significantly higher than in the control population. Further studies will be required to assess the clinical significance of these positive antibodies.
Language	English
Publishing date	2017-07-26
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1231070-0
ISSN	2191-0251 ; 0334-018X
ISSN (online)	2191-0251
ISSN	0334-018X
DOI	10.1515/jpem-2017-0011
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Zs.A 2258: Show issues

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Article ; Online: High prevalence of organ specific autoantibodies in Indian type 1 diabetic patients.

Channabasappa, Shivaprasad / Kolly, Anish / Pulikkal, Annie / Kumar, K M Prasanna

Journal of pediatric endocrinology & metabolism : JPEM

2017

Abstract	Background: Type 1 diabetes (T1D) is frequently associated with other autoimmune conditions such as autoimmune thyroiditis, coeliac disease (CD) and Addison's disease. There are sparse data on the prevalence of antibodies against these conditions in Indian patients with T1D. This study aims to evaluate prevalence of these T1D associated autoantibodies in Indian patients. Methods: Two hundred and fifty-eight patients with T1D were recruited from the Bangalore Diabetes Hospital and the Vydehi Institute of Medical Sciences and Research Centre (VIMS) for the study. Participants diagnosed with diabetes before the age of 18 years, as per the American Diabetes Association (ADA) criteria, and who were classified as T1D based on clinical grounds were recruited for the study. Anti-thyroid peroxidase antibody (TPO) and IgA tissue transglutaminase antibody (tTG) were estimated in all the patients. 21-Hydroxylase antibody (21-OHAb) were estimated in 170 patients. All assays were done by commercial immunoassay. Eighty-eight unrelated age-matched healthy controls were chosen for comparison. Results: The mean age of T1D patients was 14.33 years. The mean duration of diabetes was 4.88 years. Anti-TPO was positive in 43 (16.7%) patients with T1D as compared to 3 (3.4%) in controls. IgA tTG was positive in 12 (4.65%) patients with T1D and was absent in controls. 21-OHAb was positive in two (1.1%) patients with T1D and was absent in controls. Both patients who had positive 21-OHab had the other two antibodies. Five patients had positive anti-TPO and IgA-tTG antibodies. Conclusions: Anti-TPO antibody was the most prevalent antibody in patients with T1D. Anti-TPO and IgA-tTG antibodies were significantly higher than in the control population. Further studies will be required to assess the clinical significance of these positive antibodies.
Language	English
Publishing date	2017-06-23
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1231070-0
ISSN	2191-0251 ; 0334-018X
ISSN (online)	2191-0251
ISSN	0334-018X
DOI	10.1515/jpem-2017-0011
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Zs.A 2258: Show issues

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ab Jg. 2022: Lesesaal (EG)

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Article: Till Surgery do us Part: Unexpected Bilateral Kissing Molars.

Anish, Narayanankutty / Vivek, Velayudhannair / Thomas, Sunila / Daniel, Vineet Alex / Thomas, Jincy / Ranimol, Prasanna

Clinics and practice

2015 Volume 5, Issue 1, Page(s) 688

Abstract: The occurrence impacted teeth, single or multiple is very common. But, phenomenon of kissing molars is an extremely rare phenomenon. Mandibular third molars are the most common impacted teeth. Mandibular first or second molars does not share the same ... ...

Abstract	The occurrence impacted teeth, single or multiple is very common. But, phenomenon of kissing molars is an extremely rare phenomenon. Mandibular third molars are the most common impacted teeth. Mandibular first or second molars does not share the same frequency of occurrence. But, there are rare cases in which the occlusal surfaces of impacted molars are united by the same follicular space and the roots point in the opposite direction, and are termed as kissing molars. Sometimes, these teeth will be associated with pathologies. This article reports a rare case of mandibular bilateral kissing molars.
Language	English
Publishing date	2015-02-02
Publishing country	Italy
Document type	Case Reports
ZDB-ID	2605724-4
ISSN	2039-7283 ; 2039-7275
ISSN (online)	2039-7283
ISSN	2039-7275
DOI	10.4081/cp.2015.688
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Article: Corporate governance and stock market liquidity in India

Prasanna, P. Krishna / Menon, Anish S

International journal of behavioural accounting and finance : IJBAF Vol. 3, No. 1/2 , p. 24-45

2012 Volume 3, Issue 1, Page(s) 24–45

Author's details	P. Krishna Prasanna and Anish S. Menon
Keywords	Corporate Governance ; Aktienmarkt ; Liquidität ; Indien
Language	English
Size	graph. Darst.
Publisher	Inderscience Enterprises
Publishing place	Bath [u.a.]
Document type	Article
ZDB-ID	2471858-0
ISSN	1753-1969
Database	ECONomics Information System

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