"SNP and STR analysis using NGS
Niels Morling, MD DMSc
Professor of Forensic Genetics
Chairman & Director
Department of Forensic Medicine
Faculty of Health and Medical Sciences
University of Copenhagen
Denmark"
It is the DNA located in the mitochondria.Mitochondrial DNA (mtDNA or mDNA) is the DNA located in the mitochondria.
They are double stranded circular DNA molecule.
It is only 16 kb in length – contains 16,600 bp.
It is haploid in nature.
It codes for 37 genes.
13 genes provide instructions for making enzymes involved in oxidative phosphorylation.
It is a process that uses oxygen and simple sugars to create ATP, the cells main energy source.
"SNP and STR analysis using NGS
Niels Morling, MD DMSc
Professor of Forensic Genetics
Chairman & Director
Department of Forensic Medicine
Faculty of Health and Medical Sciences
University of Copenhagen
Denmark"
It is the DNA located in the mitochondria.Mitochondrial DNA (mtDNA or mDNA) is the DNA located in the mitochondria.
They are double stranded circular DNA molecule.
It is only 16 kb in length – contains 16,600 bp.
It is haploid in nature.
It codes for 37 genes.
13 genes provide instructions for making enzymes involved in oxidative phosphorylation.
It is a process that uses oxygen and simple sugars to create ATP, the cells main energy source.
Techniques of DNA Extraction, Purification and QuantificationBHUMI GAMETI
Introduction
The overall process…
Uses of isolated genomic DNA
Extraction of DNA from plant material
Components of DNA extraction solutions
Cell Lysis or Cell disruption :
Purification of DNA
CTAB Method
Phenol–chloroform extraction
PROTEINASE K
Salting out
Silica adsorption method
Magnetic beads
FTA Paper
Nucleic acid quantification
Agarose Gel Electrophoresis
UV spectroscopy
DNA quantification using NanoDrop
Gene mapping means the mapping of genes to specific locations on chromosomes.
Such maps indicates the positions of genes in the genome and also distance between them.
Genetic and environmental factors are the two keys that make human phenotype variations. When the genomic DNA sequences on equivalent chromosomes of any two individuals are compared, there is substantial variation in the sequence at many points throughout the genome. The term polymorphism was originally used to describe variations in shape and form that distinguish normal individuals within a species from each other. These days, geneticists use the term genetic polymorphisms to describe the inter-individual, functionally silent differences in DNA sequence that make each human genome unique. In order to better understand the phenomenon of genetic polymorphism, an emphasis has been laid on the structures and functions of nucleotides, genes and nucleic acids, including their relationship with polymorphism.
Polymorphism can be caused by factors such as mutation, which is defined as a permanent transmissible change in DNA sequence. Mutations are classified based on where they occur somatic and germ line mutations) and the length of the nucleotide sequences they affect (gene-level and chromosomal mutations). The various types of polymorphisms include; single nucleotide polymorphisms (SNPs), small-scale insertions/deletions, polymorphic repetitive elements, microsatellite variation and haplotypes.
Variations in DNA sequences may have a major impact on how human beings respond to disease, bacteria, viruses, toxins, chemicals, drugs, and other therapies. Many clinical phenotypes observed in diseases seem to have considerable genetic components.
Determining genetic polymorphism can be based on morphological, biochemical, and molecular types of information. However, molecular markers have advantages over other kinds, where they show genetic differences on a more detailed level without interferences from environmental factors, and where they involve techniques that provide fast results detailing genetic diversity. Some of the techniques used in studying polymorphisms include; PCR based techniques and techniques involving DNA based markers.
Key words: Genetic polymorphism, effects in a population,
Human identification from DNA is typically based
on 13 short-tandem repeat (STR) alleles. Commercial kits used in forensic casework rely on the detection of these alleles in DNA samples acquired from an individual. However, the process itself is slow (it can take up to 2 days when conducting a laboratory analysis or 1 hour when using Rapid DNA systems) and has been designed to operate on pristine DNA samples. The need for
achieving fast and accurate DNA processing has spurred efforts in developing portable systems that can reduce the processing time to less than 1 hour. But such systems are expected to operate on degraded DNA samples due to the architecture and process used by the instrument. Consequently, detecting the alleles in such degraded DNA samples can be a challenging problem. In this paper, we present an algorithm to detected allelic peaks from degraded DNA signals based on an adaptive signal processing scheme.
DNA fingerprinting is a research facility procedure used to set up a connection between natural proof and a suspect in a criminal examination. A DNA test taken from a wrongdoing scene is contrasted and a DNA test from a suspect. On the off chance that the two DNA profiles are a match, at that point the proof originated from that suspect. On the other hand, on the off chance that the two DNA profiles don't coordinate, at that point the proof can't have originated from the suspect. DNA fingerprinting is likewise used to build up paternity.
The power point presentation consists of 36 slides explaining about history, principle, different steps involved and applications of DNA fingerprinting. Recent Developments and the Future prospects of DNA profiling have also been mentioned
During DNA replication, the two parental strands separate and each acts as a template to direct the enzyme catalysed synthesis of a new com-plementary daughter strand following the base pairing rule. Three basic steps involved in DNA repli-cation are Initiation, elongation and termination.
Techniques of DNA Extraction, Purification and QuantificationBHUMI GAMETI
Introduction
The overall process…
Uses of isolated genomic DNA
Extraction of DNA from plant material
Components of DNA extraction solutions
Cell Lysis or Cell disruption :
Purification of DNA
CTAB Method
Phenol–chloroform extraction
PROTEINASE K
Salting out
Silica adsorption method
Magnetic beads
FTA Paper
Nucleic acid quantification
Agarose Gel Electrophoresis
UV spectroscopy
DNA quantification using NanoDrop
Gene mapping means the mapping of genes to specific locations on chromosomes.
Such maps indicates the positions of genes in the genome and also distance between them.
Genetic and environmental factors are the two keys that make human phenotype variations. When the genomic DNA sequences on equivalent chromosomes of any two individuals are compared, there is substantial variation in the sequence at many points throughout the genome. The term polymorphism was originally used to describe variations in shape and form that distinguish normal individuals within a species from each other. These days, geneticists use the term genetic polymorphisms to describe the inter-individual, functionally silent differences in DNA sequence that make each human genome unique. In order to better understand the phenomenon of genetic polymorphism, an emphasis has been laid on the structures and functions of nucleotides, genes and nucleic acids, including their relationship with polymorphism.
Polymorphism can be caused by factors such as mutation, which is defined as a permanent transmissible change in DNA sequence. Mutations are classified based on where they occur somatic and germ line mutations) and the length of the nucleotide sequences they affect (gene-level and chromosomal mutations). The various types of polymorphisms include; single nucleotide polymorphisms (SNPs), small-scale insertions/deletions, polymorphic repetitive elements, microsatellite variation and haplotypes.
Variations in DNA sequences may have a major impact on how human beings respond to disease, bacteria, viruses, toxins, chemicals, drugs, and other therapies. Many clinical phenotypes observed in diseases seem to have considerable genetic components.
Determining genetic polymorphism can be based on morphological, biochemical, and molecular types of information. However, molecular markers have advantages over other kinds, where they show genetic differences on a more detailed level without interferences from environmental factors, and where they involve techniques that provide fast results detailing genetic diversity. Some of the techniques used in studying polymorphisms include; PCR based techniques and techniques involving DNA based markers.
Key words: Genetic polymorphism, effects in a population,
Human identification from DNA is typically based
on 13 short-tandem repeat (STR) alleles. Commercial kits used in forensic casework rely on the detection of these alleles in DNA samples acquired from an individual. However, the process itself is slow (it can take up to 2 days when conducting a laboratory analysis or 1 hour when using Rapid DNA systems) and has been designed to operate on pristine DNA samples. The need for
achieving fast and accurate DNA processing has spurred efforts in developing portable systems that can reduce the processing time to less than 1 hour. But such systems are expected to operate on degraded DNA samples due to the architecture and process used by the instrument. Consequently, detecting the alleles in such degraded DNA samples can be a challenging problem. In this paper, we present an algorithm to detected allelic peaks from degraded DNA signals based on an adaptive signal processing scheme.
DNA fingerprinting is a research facility procedure used to set up a connection between natural proof and a suspect in a criminal examination. A DNA test taken from a wrongdoing scene is contrasted and a DNA test from a suspect. On the off chance that the two DNA profiles are a match, at that point the proof originated from that suspect. On the other hand, on the off chance that the two DNA profiles don't coordinate, at that point the proof can't have originated from the suspect. DNA fingerprinting is likewise used to build up paternity.
The power point presentation consists of 36 slides explaining about history, principle, different steps involved and applications of DNA fingerprinting. Recent Developments and the Future prospects of DNA profiling have also been mentioned
During DNA replication, the two parental strands separate and each acts as a template to direct the enzyme catalysed synthesis of a new com-plementary daughter strand following the base pairing rule. Three basic steps involved in DNA repli-cation are Initiation, elongation and termination.
Evolutionary Genetics by: Kim Jim F. Raborar, RN, MAEd(ue)Kim Jim Raborar
This presentation was created as a partial fulfillment of the requirements in the subject Advanced Genetics. Everything that was here were kinda symbolic. I mean, you could recognize that this was a product of so much data interpretation. I therefore suggest you read and read a lot first before you go back to this presentation. Or you could just contact me so i could send you the key-pointers.
Have a super nice day.
Kimy
Exploiting Artificial Intelligence for Empowering Researchers and Faculty, In...Dr. Vinod Kumar Kanvaria
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International FDP on Fundamentals of Research in Social Sciences
at Integral University, Lucknow, 06.06.2024
By Dr. Vinod Kumar Kanvaria
Executive Directors Chat Leveraging AI for Diversity, Equity, and InclusionTechSoup
Let’s explore the intersection of technology and equity in the final session of our DEI series. Discover how AI tools, like ChatGPT, can be used to support and enhance your nonprofit's DEI initiatives. Participants will gain insights into practical AI applications and get tips for leveraging technology to advance their DEI goals.
Normal Labour/ Stages of Labour/ Mechanism of LabourWasim Ak
Normal labor is also termed spontaneous labor, defined as the natural physiological process through which the fetus, placenta, and membranes are expelled from the uterus through the birth canal at term (37 to 42 weeks
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
1. Human Genetics
And Population
GeneticsSubmitted to –
Dr Sapna sharma
Dept of Genetics
MDU Rohtak
Presented by –
Deepak Saini
M sc Forensic science 4th sem
Roll no -1602
2/19/2017 1Deepak Saini
2. Genetics
• Human genetics- scientific study of human
variation and Heredity
2/19/2017 2Deepak Saini
.Genetics is the study of genes, genetic variation, and
heredity in living organisms. It is generally considered
a field of biology, but intersects frequently with many
other life sciences and is strongly linked with the study
of information systems.
3. Terms you should know
• CHROMOSOME: thread of DNA, made up of a string of
genes.
• GENE: a length of DNA that is the unit of heredity and
codes for a specific protein. A gene may be copied and
passed on to the next generation.
• ALLELE: any of two or more alternative forms of a gene.
• HAPLOID NUCLEUS: a nucleus containing a single set of
unpaired chromosomes (e.g. sperm and egg)
• DIPLOID NUCLEUS: a nucleus containing two sets of
chromosomes (e.g. in body cells)
2/19/2017 3Deepak Saini
4. Terms you should know:
• GENOTYPE: genetic makeup of an organism in term of the
alleles present ( e.g. Tt or GG).
• PHENOTYPE: physical or other features of an organism
due to both its genotype and its environment (e.g. tall
plant or green seed)
• HOMOZYGOUS: having two identical alleles of a particulat
gene (e.g. TT or gg).Two identical homozygous individuals
that breed together will be pure-breeding.
• HETEROZYGOUS: having two different alleles of a
particular gene (e.g. Tt or Gg), not pure- breeding.
• DOMINANT: an allele that is expresed if it is present
(e.g. T or G)
• RECESSIVE: an allele that is only expresses when there is
no dominant allele of the gene present. ( e.g t or g )
2/19/2017 4Deepak Saini
5. •Genes control the characteristics of living
organisms
•Genes are carried on the chromosomes
•Chromosomes are in pairs, one from each parent
•Genes are in pairs
•Genes controlling the same characteristics occupy
identical positions on corresponding chromosomes
2/19/2017 5Deepak Saini
6. 2/19/2017 Deepak Saini 6
Heredity is the genetic information passing
for traits from parents to their offspring, either
through asexual reproduction or sexual reproduction.
.This is the process by which an
offspring cell or organism acquires or becomes
predisposed to the characteristics of its parent cell or
organism. Through heredity, variations exhibited by
individuals can accumulate and cause
some species to evolve through the natural
selection of specific phenotype traits.
-The study of heredity in biology is called genetics,
7. In most populations of animals there are approximately equal
numbers of males and females.
This is the result of a pair of chromosomes; the sex chromosomes
called the X and Y chromosomes.
The X and Y chromosomes are a homologous pair but in many
animals the Y chromosome is smaller than the X.
Females have two X chromosomes in their cells.
Males have one X and one Y in their cells.
At meiosis, the sex chromosomes are separated so the the gametes
receive only one: either an X or a Y.
Sex chromosomes
2/19/2017 7Deepak Saini
9. • People have been fascinated at how children will
resemble their parents and vice versa.
• As years went by, scientists began to search for
more information on how these traits are passed
on.
• The passing of traits from parents to offspring is
HEREDITY and the science that deals with the
study of heredity is GENETICS.
2/19/2017 9Deepak Saini
10. • In human,
chromosom
es number 1
is the
biggest
containing
8,000 genes
and
chromosom
es 21 is the
smallest
with 300
genes.
In short, the 44 chromosomes are autosomes andes.
2/19/2017 10Deepak Saini
11. Mutation
• - is a change of the nucleotide sequence of the
genome of an organism, virus, or extra
chromosomal genetic element.
• Mutations result from errors during DNA
replication or other types of damage to DNA.
2/19/2017 11Deepak Saini
13. Substitution
A substitution is a mutation
that exchanges one base for
another (i.e., a change in a
single "chemical letter" such as
switching an A to a G).
2/19/2017 13Deepak Saini
17. Inversion
a DNA sequence of
nucleotides is reversed.
Inversions can occur among a
few bases within a gene or
among longer DNA sequences
that contain several genes.
2/19/2017 17Deepak Saini
21. Frameshift
Since protein-coding DNA is
divided into codons three bases
long, insertions and deletions
can alter a gene so that its
message is no longer correctly
parsed.
2/19/2017 21Deepak Saini
23. Gene Mutation
is a permanent change in the
DNA sequence that makes up a
gene. Mutations range in size from
a single DNA building block (DNA
base) to a large segment of a
chromosome.
2/19/2017 23Deepak Saini
24. Inherited
• hereditary mutations or germline
mutations
• This type of mutation is present
throughout a person’s life in
virtually every cell in the body.
2/19/2017 24Deepak Saini
25. Acquired
• or somatic mutations
• occur in the DNA of individual cells
at some time during a person’s life.
• caused by environmental factors
• cannot be passed on to the next
generation.
2/19/2017 25Deepak Saini
26. Natural cause
• DNA fails to copy accurately
–when a cell divides, it makes a
copy of its DNA and sometimes
the copy is not quite perfect.
2/19/2017 26Deepak Saini
27. External Influences/Mutagens
• In genetics, a mutagen is a
physical or chemical agent that
changes the genetic material,
usually DNA, of an organism and
thus increases the frequency of
mutations above the natural
background level.
2/19/2017 27Deepak Saini
29. Population genetics
• Investigates genetic variation among individuals
within groups (populations, gene pools).
• Examines the genetic basis for evolutionary
change and seeks to understand how patterns
vary geographically and through time.
2/19/2017 29Deepak Saini
30. • Different types of population genetics:
– Empirical population genetics: measures and
quantifies aspects of genetic variation in
populations.
– Theoretical population genetics: explains variation
in terms of mathematical models of the forces that
change allele frequencies (genetics drift, selection,
gene flow, etc.).
2/19/2017 30Deepak Saini
31. Types of questions studied by population geneticists:
• How much variation occurs in natural populations, and
what processes control the variation observed?
• How does geography and dispersal behavior shape
population structure?
• What forces are responsible for population differentiation
and how do they affect genetic diversity?
• Mutation genetic diversity
• Selection genetic diversity
• Genetic drift genetic diversity
• Migration genetic diversity
• Non-random mating genetic diversity
• Recombination genetic diversity2/19/2017 31Deepak Saini
32. Population Genetics:
• One of the oldest and richest examples of success of
mathematical theory in biology.
• Provided synthesis of Mendelian genetics and
Darwinian natural selection in the first part of the 20th
century “modern synthesis”.
• Modern synthesis is the foundation for modern
evolutionary biology and population genetics.
2/19/2017 32Deepak Saini
33. Laid the first early groundwork the modern synthesis:
Charles Darwin 1809-1882
The Origin of Species
Alfred Russell Wallace 1823-1913
“Wallace’s Line”
Thomas H. Huxley 1825-1895
“Darwin’s Bulldog”
2/19/2017 33Deepak Saini
34. Theoretical/mathematical population geneticists:
Ronald A. Fisher 1890-1962
The Genetical Theory of Natural Selection
J. B. S. Haldane 1892-1964
The Causes of Evolution
Sewall Wright 1889-1988
Evolution and the Genetics of Populations - 4 vol.
2/19/2017 34Deepak Saini
35. Architects the modern synthesis, extended theoretical work of Fisher, Haldane, and
Wright to real organisms:
Theodosius Dobzhansky 1900-1975
Genetics and the Origin of Species
Julian Huxley 1887-1975
Evolution: The Modern Synthesis
Ernst Mayr 1904-2005
Systematics and the Origin of Species
“Biological Species Concept”
George G. Simpson 1902-1984
Tempo and Mode in Evolution
George L. Stebbins 1906-2000
Variation and Evolution
in Plants
2/19/2017 35Deepak Saini
36. Ways to describe genetic structure of populations:
Genotypic frequency
• Count individuals with one genotype and divide by total
number of individuals. Repeat for each genotype in the
population:
f(BB) = 452/497 = 0.909
f(Bb) = 43/497 = 0.087
f(bb) = 2/497 = 0.004
Total = 1.000
2/19/2017 36Deepak Saini
37. Ways to describe genetic structure of populations:
Allelic frequency
• Allelic frequencies offer more information than genotypic
frequencies and can be calculated in two different ways:
1. Allele (gene) counting method:
p = f(A) = (2 x count of AA) + (1 count of Aa)/ 2 x total number of
individuals
2. Genotypic frequency method:
p = f(A) = (frequency of the AA homozygote) + (1/2 x frequency of the
Aa heterozygote)
p = f(a) = (frequency of the aa homozygote) + (1/2 x frequency of the Aa
heterozygote)
2/19/2017 37Deepak Saini
38. Allelic frequencies with multiple alleles:
Example: A1, A2, and A3
p = f(A1) = (2 x A1A1) + (A1A2) + (A1A3)/2 x total individuals
q = f(A2) = (2 x A2A2) + (A1A2) + (A2A3)/2 x total individuals
r = f(A3) = (2 x A3A3) + (A1A3) + (A2A3)/2 x total individuals
Or
p = f(A1) = f(A1A1) +f(A1A2)/2 + f(A1A3)/2
q = f(A2) = f(A2A2) + f(A1A2)/2 + f(A2A3)/2
r = f(A3) = f(A3A3) + f(A1A3)/2 + f(A2A3)/2
2/19/2017 38Deepak Saini
39. Allelic frequencies at X-linked loci:
Females have 2 X-linked alleles, and males have 1 X-linked allele.
p = f(XA) = (2 x XA XA females) + (XA Xa females) + (XA Y males)/
(2 x # females) + (# males)
q = f(Xa) = (2 x Xa Xa females) + (XA Xa females) + (Xa Y males)/
(2 x # females) + (# males)
If number of females and males are equal:
p = f(XA) = 2/3[f(XAXA) +1/2f(XAXa)] + 1/3f(XAY)
q = f(Xa) = 2/3[f(XaXa) +1/2f(XAXa)] + 1/3f(XaY)
2/19/2017 39Deepak Saini
40. Hardy-Weinberg law:
• Independently discovered by Godfrey H. Hardy
(1877-1947) and Wilhelm Weinberg (1862-
1937).
• Explains how Mendelian segregation influences
allelic and genotypic frequencies in a population.
2/19/2017 40Deepak Saini
42. Assumptions:
1. Population is infinitely large, to avoid effects of genetic
drift (= change in genetic frequency due to chance).
2. Mating is random (with regard to traits under study).
3. No natural selection (for traits under study).
4. No mutation.
5. No migration.
2/19/2017 42Deepak Saini