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Course Detail

Course Name Statistical Methods in Diagnostics
Course Code 25CLG503
Program M. Sc. Clinical Genomics
Semester 1
Credits 1
Campus Kochi

Syllabus

Unit 1

(Lectures 05)

Introduction to Biostatistics in Clinical Genomics. Importance of statistics in diagnostics and genomic medicine. Types of diagnostic data in genomics: SNPs, CNVs, expression levels.

Types of Data and Descriptive Statistics: Nominal, ordinal, interval, ratio in genomics (e.g., genotype vs expression). Descriptive statistics: mean, median, variance, standard deviation, Study Designs in Diagnostic Genomics: cross-sectional, cohort, case-control, Sampling methods and sample size estimation.

Unit 2

(Lectures 05)

Probability and Probability Distributions in Genomics: Basics of probability in genetic testing. Normal, binomial, Poisson distributions in mutation modelling. Hardy-Weinberg equilibrium as a probability model. Hypothesis Testing in Genomic Diagnostics: Null and alternative hypotheses in SNP association. p-values, Type I/II errors. Parametric and non-parametric methods for genomic data (e.g., t-test, Mann-Whitney). Diagnostic Accuracy Metrics: Sensitivity, specificity, Positive Predictive Value (PPV) and Negative Predictive Value (NPV). Likelihood ratios and diagnostic odds ratio in rare variant detection. Impact of prevalence on test performance

Unit 3

(Lectures 05)

Application to Genomic Tests (Binary and Continuous): Interpretation of gene expression-based diagnostics (Oncotype DX, etc.). ROC Curve Analysis in Genomic Biomarkers: ROC curves and AUC for gene panels and NGS-based tests. Limitations of AUC in genomics. Regression and Predictive Modeling in Diagnostics, Linear and logistic regression basics, Multivariate modeling: feature selection, interaction terms, Model validation: internal and external, Introduction to survival analysis in diagnostic context (Kaplan-Meier, Cox regression), predictive models for diagnostic applications using real-world datasets. Statistical Software, Case Studies, and Reporting Standards, Hands-on data analysis using R/SPSS/GraphPad, Case studies from infectious diseases, cancer, and genetic diagnostics, STARD guidelines for reporting diagnostic accuracy studies, Critical appraisal of diagnostic literature, Ethical use and interpretation of diagnostic statistics.

Introduction

Total number of classes: 15

Preamble

Statistical Methods in Diagnostics provides a foundation in statistical tools and techniques used in biomedical research and diagnostics. The course focuses on experimental design, data interpretation, and statistical validation of diagnostic tests. Students will gain hands-on experience using software tools and statistical methods for sensitivity, specificity, ROC analysis, and predictive modelling.

Objectives and Outcomes

Course outcomes

CO1: To apply biostatistics and diagnostic study designs, including data types and sampling methods.

CO2: To understand probability, distributions, and hypothesis testing, including parametric and non-parametric tests.

CO3: To evaluate diagnostic test accuracy using sensitivity, specificity, and predictive values.

CO4: To interpret ROC curves, AUC, and optimize diagnostic test cut-off points.

CO5: To apply regression and predictive modeling techniques, including survival analysis in diagnostics.

CO6: To use statistical software for data analysis, case studies, and adhere to reporting standards.

Program outcome

PO1: Bioscience Knowledge

PO2: Problem Analysis

PO3: Design/Development of Solutions

PO4: Conduct Investigations of complex problems

PO5: Modern tools usage

PO6: Bioscientist and Society

PO7: Environment and Sustainability

PO8: Ethics

PO9: Individual & Team work

PO10: Communication

PO11: Project management & Finance

PO12: Lifelong learning

0 – No affinity; 1 – low affinity; 2 – Medium affinity; 3 – High affinity

CO-PO Mapping Table:

COs PO1 PO2 PO3 PO4 PO5 PO6 PO7 PO8 PO9 PO10 PO11 PO12
CO1 3 3 2 2 2 2 1 1 3
CO2 3 3 2 3 2 1 3
CO3 3 3 3 3 2 1 3
CO4 2 2 3 3 2 1 2
CO5 3 3 3 3 3 1 3
CO6 2 3 3 3 3 1 1 2 2 3

Program Specific Outcomes (PSO):

PSO1. Apply fundamental molecular biology principles to interpret clinical genomic data.

PSO2. Use molecular techniques (e.g., PCR, RT-PCR, sequencing) to detect genetic mutations and biomarkers.

PSO3. Analyze genotype-phenotype correlations in inherited and acquired disorders.

PSO4. Identify pathogenic variants from NGS data and interpret their clinical relevance.

PSO5. Correlate molecular pathways with disease mechanisms and therapeutic targets.

PSO6. Develop and validate diagnostic assays based on molecular biology principles.

PSO7. Utilize molecular biology to support pharmacogenomic profiling and therapy optimization.

PSO8. Integrate multi-omic data (genomic, transcriptomic, epigenomic) for personalized health solutions.

PSO9. Apply molecular knowledge to cancer genomics, infectious diseases, and rare genetic disorders.

PSO10. Translate molecular discoveries into clinical interventions through evidence-based practice.

0 – No affinity; 1 – low affinity; 2 – Medium affinity; 3 – High affinity

CO-PSO Mapping Table:

COs PSO1 PSO2 PSO3 PSO4 PSO5 PSO6 PSO7 PSO8 PSO9 PSO10
CO1 2 2 2 1 2 1 2
CO2 2 2 3 2
CO3 3 3 3 2 3
CO4 2 2 2 2 2
CO5 3 3 3 2 2 2 2 3
CO6 2 3 3 2 2 3

Evaluation Pattern

Evaluation Pattern: 50+50 = 100

Internal Assessment – 50% 
Periodical 1 Exam 20% 
Periodical 2 Exam 20% 
Continuous Assessment  Assignment/Test/Quiz 10% 
  50%
End Semester Examination- 50%
Theory Exam 50%  
  50%
Total 100%

Textbooks / References

Textbook:

Zhou XH, Obuchowski NA, McClish DK. Statistical Methods in Diagnostic Medicine. 2nd ed. Hoboken (NJ): Wiley; 2011.

Reference Book:

Altman DG. Practical Statistics for Medical Research. London: Chapman and Hall/CRC; 1991.

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