Introduction to Bioinformatics and Diagnostics

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Questions and Answers

What is one of the primary advantages of molecular diagnostics?

Increased complexity in analysis

Higher costs

Improvement in sensitivity (correct)

Increased time for results

What is the purpose of amniocentesis in genetic testing?

To evaluate kidney function

To assess for metabolic disorders

To test for infectious diseases

To detect chromosome abnormalities (correct)

How does fluorescence in situ hybridization (FISH) assist in genetic diagnostics?

By amplifying DNA

By using fluorescence probes specific for chromosomes and genes (correct)

By separating RNA from DNA

By conducting enzyme assays

What is a significant characteristic of the 'probe' in a hybridization assay?

It carries a marker for detection Signup and view all the answers

What type of mutation does the RFLP method primarily detect in sickle cell disease?

Point mutations Signup and view all the answers

What is the main purpose of dot blot assays?

To detect single nucleotide polymorphisms (SNPs) Signup and view all the answers

Which statement accurately describes hybridization in molecular diagnostics?

It involves the interaction of single-stranded oligonucleotides Signup and view all the answers

What is the result of a positive RFLP test in the context of sickle cell disease?

Presence of a sickle cell mutation Signup and view all the answers

What is the primary function of the Allele-Specific Oligonucleotide (ASO) Dot Blot technique?

To detect specific alleles associated with genetic diseases Signup and view all the answers

What distinguishes the Reverse Dot Blot from the ASO Dot Blot?

It employs an array of ASOs that bind to labeled target DNA. Signup and view all the answers

Why are Single Nucleotide Polymorphisms (SNPs) significant in the human genome?

They occur every 1,000-3,000 base pairs. Signup and view all the answers

What technique is used to measure the binding intensity of a patient’s DNA to an SNP or gene on a microarray?

Laser scanning Signup and view all the answers

What is the main application of microarray technology in the medical field?

Comparing levels of gene expression Signup and view all the answers

In microarray analysis, what does the binding of a patient’s fluorescently tagged DNA to a gene sequence signify?

The presence of a specific mutation or SNP Signup and view all the answers

How often does a SNP occur in the human genome?

Every 1,000-3,000 base pairs Signup and view all the answers

What is the role of the SNP Consortium in genomic research?

To catalog and analyze SNP variations across different populations Signup and view all the answers

Study Notes

Introduction to Bioinformatics

Bioinformatics is the application of statistics and computer science to molecular biology
It involves organizing biological data and extracting relevant information.

Detecting Genetic Diseases

Fetal testing identifies chromosome abnormalities and defective genes
- Amniocentesis (16 weeks, karyotype)
- Chorionic villus sampling (8-10 weeks, karyotype)
Testing for chromosome abnormalities and defective genes also involves:
- Fluorescence in situ hybridization (FISH)
  - Uses fluorescent probes specific to chromosomes or genes
- Spectral karyotyping

Molecular Diagnostics

Molecular diagnostics uses DNA, RNA, and proteins to detect, diagnose, subclassify, predict the course of disease, and monitor responses to treatment.
Advantages include improved sensitivity, high specificity, lower cost, and faster analysis time.

Microarray Technology

Microarrays are chips with thousands of single-stranded DNA molecules.
DNA from a patient is isolated, labeled, hybridized to the microarray
A laser scanner measures the fluorescence intensity to identify SNPs or genes the patient's DNA binds to.
Used to compare gene expression levels between different tissues and is applied to cancer research.

Allele-Specific Oligonucleotide (ASO) Dot Blot

A method used to detect SNPs and disease markers.
PCR amplified DNA is blotted onto a membrane, unbound probes are washed off, and bound probes are detected by radioactive or colorimetric assays.
Applied for detection of sickle cell anemia

Reverse Dot Blot

Instead of binding DNA to the membrane, an array of ASOs (allele-specific oligonucleotides) is bound to a membrane and hybridized to labeled target DNA.
Used to analyze patient DNA for genetic markers/mutations.

Single Nucleotide Polymorphisms (SNPs)

SNPs are one of the most common forms of genetic variation.
Roughly one SNP occurs every 1,000-3,000 base pairs (bp) in human DNA.
Most SNPs are located in non-coding regions (introns).
SNPs influence traits and diseases.
10 pharmaceuticals donated millions to the SNP Consortium.

Genome-Wide Association Studies (GWAS)

GWAS compare genomic DNA from large samples of cases and controls to identify SNPs correlated with specific traits or diseases.
Sites differing significantly between cases and controls are validated in independent samples.
Used to identify links between genetic markers and diseases.

The HapMap Project

A public database containing over one million common genetic variations (SNPs) from four human populations.
It was crucial in advancing genome-wide association studies.

Bioinformatics Databases

GeneBank/DDBJ/EMBL: Nucleotide sequence data
Ensembl: Human and mouse genome data
PubMed: Literature references and abstracts
Swiss-Prot: Protein sequences of known function
OMIM: Catalog of human genetic diseases

Genome De Novo Sequencing (NGS)

NGS is used to sequence whole genomes.
Used for genomic studies using fragments of DNA.
Steps in the NGS process: fragment and sequence, prepare and sequence reads, remove low coverage regions, break up the contigs and create scaffolds/assemble sequences from contigs and scaffolds, and closing gaps in scaffolds.

Bioinformatics Analysis

SOAP Alignment, InDel Detection & Annotation, SNP Detection & Annotation, etc.
Individual re-sequencing, HGMD analysis and Haplotypes construction are examples of optional bioinformatics analyses.

Medical Products and Applications of Biotechnology

Microarray technology is a method for analyzing the expression of genes in different tissues.
This technique is applied to cancer research and many other biotech fields.

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Description

This quiz covers key topics in bioinformatics, including molecular diagnostics and genetic disease detection techniques. You'll learn about tools like microarrays, amniocentesis, and fluorescence in situ hybridization. Assess your understanding of the application of statistics and computer science in biology.