This study sequenced four genes (TNNT3, TNNI2, TPM2, MYH3) in 19 individuals with distal arthrogryposis (DA) to search for pathogenic mutations. No mutations were found in the sequenced regions for the 13 individuals with unclassified DA or 5 with Sheldon-Hall syndrome. A previously reported pathogenic mutation in MYH3 was identified in the single individual with Freeman-Sheldon syndrome, providing further evidence that mutations in this gene cause this condition. The results suggest that mutations in other regions of the genes or in non-coding regions may be responsible for the unclassified DA cases.
Epigenetic silencing of MGMT (O6-methylguanine DNA methyltransferase) gene in...arman170701
O6–methylgunine-DNA methyltransferace (MGMT) is a DNA binding protein that is involved in repairing mutations.
MGMT gene - a tumor suppressor gene that codes MGMT (O6-methylguanine DNA methyltransferase) protein.
The MGMT protein removes mutagenic methyl groups from guanines through the methyltransferase activity.
Epigenetic silencing of MGMT (O6-methylguanine DNA methyltransferase) gene in...arman170701
O6–methylgunine-DNA methyltransferace (MGMT) is a DNA binding protein that is involved in repairing mutations.
MGMT gene - a tumor suppressor gene that codes MGMT (O6-methylguanine DNA methyltransferase) protein.
The MGMT protein removes mutagenic methyl groups from guanines through the methyltransferase activity.
KDM5 epigenetic modifiers as a focus for drug discoveryChristopher Wynder
A summary presentation of my scientific work.
My laboratory focused on an enzyme KDM5b (aka PLU-1, JARID1b) that was widely expressed during development and played a key role in progression of breast cancer through HER-2.
My lab focused on understanding the key biochemical activity of the enzyme through dissecting the proteomic and genomic interactors.
Our results were confirmed through the use of ES cells, adult stem cells and mouse models.
Much of this work remains unpublished, please contact me for more information and/or access to any reagents that I still have as part of this work.
crwynder@gmail.com
Genetic polymorphism and It's Applicationsawaismalik78
Genetic polymorphism
Genetic polymorphism is the inheritance of a trait controlled by a single genetic locus with two alleles, in which the least common allele has a frequency of about 1% or greater. Genetic polymorphism is a difference in DNA sequence among individuals, groups, or populations.
Types of polymorphisms
Protein/enzyme polymorphisms
In the early days of human genetics, majority of polymorphisms were those associated with proteins and enzymes. To detect the polymorphism and a person’s genotype, one performed assays for the gene product, i.e., the protein or enzyme produced by the genetic blueprint.
DNA polymorphisms
The large class of polymorphisms are those that detect Slight variations at the level of DNA nucleotides.
Single nucleotide polymorphisms
A single nucleotide polymorphism or SNP is a sequence of DNA on which humans vary by one and only one nucleotide . Because humans differ by one nucleotide per every thousand or so nucleotides, there are millions of SNPs scattered throughout the human genome.
Tandem repeat polymorphisms
A tandem repeat polymorphism consists of a series of nucleotides that are repeated in tandem (i.e., one time after another). The polymorphism consists of the number of repeats.
Restriction Fragment Length Polymorphism (RFLP)
Restriction Fragment Length Polymorphism (RFLP) is a type in which organisms may be differentiated by analysis of patterns derived from cleavage of their DNA. If two organisms differ in the distance between sites of cleavage of a particular restriction endonuclease, the length of the fragments produced will differ when the DNA is digested with a restriction enzyme.
Applications of Genetic Polymorphism
The study of polymorphism has many uses in medicine, biological research, and law enforcement. Genetic diseases may be caused by a specific polymorphism. Scientists can look for these polymorphisms to determine if a person will develop the disease, or risks passing it on to his or her children.
The role of DNA methylation in complex diseasesJordana Bell
A 1-hour lecture to 4th-year undergraduate and/or MSc students in human genetics, focusing on exploring the role of DNA methylation in human complex disease.
Plant epigenetic memory in plant growth behavior and stress response. Sally M...CIAT
Speaker: Sally Mackenzie, Lloyd and Dottie Huck Chair for Functional Genomics, Department of Biology, Pennsylvania State University. Fellow in the American Society of Plant Biologists and the American Association for the Advancement of Science (AAAS).
Event: Robert D. Havener Seminar on “Innovations for Crop Productivity”.
http://ciat.cgiar.org/event/robert-d-havener-seminar-on-innovations-for-crop-productivity/
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,
KDM5 epigenetic modifiers as a focus for drug discoveryChristopher Wynder
A summary presentation of my scientific work.
My laboratory focused on an enzyme KDM5b (aka PLU-1, JARID1b) that was widely expressed during development and played a key role in progression of breast cancer through HER-2.
My lab focused on understanding the key biochemical activity of the enzyme through dissecting the proteomic and genomic interactors.
Our results were confirmed through the use of ES cells, adult stem cells and mouse models.
Much of this work remains unpublished, please contact me for more information and/or access to any reagents that I still have as part of this work.
crwynder@gmail.com
Genetic polymorphism and It's Applicationsawaismalik78
Genetic polymorphism
Genetic polymorphism is the inheritance of a trait controlled by a single genetic locus with two alleles, in which the least common allele has a frequency of about 1% or greater. Genetic polymorphism is a difference in DNA sequence among individuals, groups, or populations.
Types of polymorphisms
Protein/enzyme polymorphisms
In the early days of human genetics, majority of polymorphisms were those associated with proteins and enzymes. To detect the polymorphism and a person’s genotype, one performed assays for the gene product, i.e., the protein or enzyme produced by the genetic blueprint.
DNA polymorphisms
The large class of polymorphisms are those that detect Slight variations at the level of DNA nucleotides.
Single nucleotide polymorphisms
A single nucleotide polymorphism or SNP is a sequence of DNA on which humans vary by one and only one nucleotide . Because humans differ by one nucleotide per every thousand or so nucleotides, there are millions of SNPs scattered throughout the human genome.
Tandem repeat polymorphisms
A tandem repeat polymorphism consists of a series of nucleotides that are repeated in tandem (i.e., one time after another). The polymorphism consists of the number of repeats.
Restriction Fragment Length Polymorphism (RFLP)
Restriction Fragment Length Polymorphism (RFLP) is a type in which organisms may be differentiated by analysis of patterns derived from cleavage of their DNA. If two organisms differ in the distance between sites of cleavage of a particular restriction endonuclease, the length of the fragments produced will differ when the DNA is digested with a restriction enzyme.
Applications of Genetic Polymorphism
The study of polymorphism has many uses in medicine, biological research, and law enforcement. Genetic diseases may be caused by a specific polymorphism. Scientists can look for these polymorphisms to determine if a person will develop the disease, or risks passing it on to his or her children.
The role of DNA methylation in complex diseasesJordana Bell
A 1-hour lecture to 4th-year undergraduate and/or MSc students in human genetics, focusing on exploring the role of DNA methylation in human complex disease.
Plant epigenetic memory in plant growth behavior and stress response. Sally M...CIAT
Speaker: Sally Mackenzie, Lloyd and Dottie Huck Chair for Functional Genomics, Department of Biology, Pennsylvania State University. Fellow in the American Society of Plant Biologists and the American Association for the Advancement of Science (AAAS).
Event: Robert D. Havener Seminar on “Innovations for Crop Productivity”.
http://ciat.cgiar.org/event/robert-d-havener-seminar-on-innovations-for-crop-productivity/
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,
Next Generation Sequencing and its Applications in Medical Research - Frances...Sri Ambati
The so-called “next-generation” sequencing (NGS) technologies allows us, in a short time and in parallel, to sequence massive amounts of DNA, overcoming the limitations of the original Sanger sequencing methods used to sequence the first human genome. NGS technologies have had an enormous impact on biomedical research within a short time frame. This talk will give an overview of these applications with specific examples from Mendelian genomics and cancer research. #h2ony
Los días 11 y 12 de diciembre de 2014, la Fundación Ramón Areces celebró el Simposio Internacional 'Neuropatías periféricas hereditarias. Desde la biología a la terapéutica' en colaboración con CIBERER-ISCIII y el Centro de Investigación Príncipe Felipe. El tipo más común de estas patologías es la enfermedad de Charcot-Marie-Tooth, un trastorno neuromuscular hereditario con una prevalencia estimada de 17-40 afectados por 100.000 habitantes. Durante estos dos días, investigadores mostraron sus avances en la mejora del diagnóstico y el tratamiento y, por ende, de la aproximación clínica y la calidad de vida de las personas afectadas por estas patologías.
Prenatal Diagnosis of Denys-Drash Syndromenavasreni
Denys-Drash syndrome consists of the triad of progressive nephropathy characterised by diffuse
mesangial sclerosis (DMS), genital abnormalities, and Wilms tumour. Nephropathy may range
from early onset proteinuria to nephrotic syndrome to end stage renal failure. Genital malformations affects both external and internal genitalia. It may range from penoscrotal hypospadias,
bilateral cryptorchidism to an enlarged clitoris with fused labia and a urogenital sinus to atrophic
uterus to streak ovaries or dysgenetic testes. The risk of developing Wilms’ tumor may be as high
as 50%.
Denys-Drash syndrome consists of the triad of progressive nephropathy characterised by diffuse mesangial sclerosis (DMS), genital abnormalities, and Wilms tumour. Nephropathy may range from early onset proteinuria to nephrotic syndrome to end stage renal failure. Genital malformations affects both external and internal genitalia...
Prenatal Diagnosis of Denys-Drash Syndromepateldrona
Denys-Drash syndrome consists of the triad of progressive nephropathy characterised by diffuse mesangial sclerosis (DMS), genital abnormalities, and Wilms tumour. Nephropathy may range from early onset proteinuria to nephrotic syndrome to end stage renal failure. Genital malformations affects both external and internal genitalia...
Prenatal Diagnosis of Denys-Drash Syndromeeshaasini
Denys-Drash syndrome consists of the triad of progressive nephropathy characterised by diffuse
mesangial sclerosis (DMS), genital abnormalities, and Wilms tumour. Nephropathy may range
from early onset proteinuria to nephrotic syndrome to end stage renal failure. Genital malformations affects both external and internal genitalia. It may range from penoscrotal hypospadias,
bilateral cryptorchidism to an enlarged clitoris with fused labia and a urogenital sinus to atrophic
uterus to streak ovaries or dysgenetic testes. The risk of developing Wilms’ tumor may be as high
as 50%.
Prenatal Diagnosis of Denys-Drash Syndromegeorgemarini
Denys-Drash syndrome consists of the triad of progressive nephropathy characterised by diffuse mesangial sclerosis (DMS), genital abnormalities, and Wilms tumour. Nephropathy may range from early onset proteinuria to nephrotic syndrome to end stage renal failure. Genital malformations affects both external and internal genitalia...
Prenatal Diagnosis of Denys-Drash SyndromeSarkarRenon
Denys-Drash syndrome consists of the triad of progressive nephropathy characterised by diffuse mesangial sclerosis (DMS), genital abnormalities, and Wilms tumour. Nephropathy may range from early onset proteinuria to nephrotic syndrome to end stage renal failure.
Prenatal Diagnosis of Denys-Drash SyndromeAnonIshanvi
Denys-Drash syndrome consists of the triad of progressive nephropathy characterised by diffuse mesangial sclerosis (DMS), genital abnormalities, and Wilms tumour. Nephropathy may range from early onset proteinuria to nephrotic syndrome to end stage renal failure. Genital malformations affects both external and internal genitalia...
Prenatal Diagnosis of Denys-Drash Syndromekomalicarol
Denys-Drash syndrome consists of the triad of progressive nephropathy characterised by diffuse
mesangial sclerosis (DMS), genital abnormalities, and Wilms tumour. Nephropathy may range
from early onset proteinuria to nephrotic syndrome to end stage renal failure. Genital malformations affects both external and internal genitalia. It may range from penoscrotal hypospadias,
bilateral cryptorchidism to an enlarged clitoris with fused labia and a urogenital sinus to atrophic
uterus to streak ovaries or dysgenetic testes. The risk of developing Wilms’ tumor may be as high
as 50%.
1. Materials and Methods
Sequencing of Distal Arthrogryposis (DA) candidate genes in patients with Freeman-Sheldon,
Sheldon-Hall, and unclassified DA syndromes
Whitney S. Best1, Kathryn M. Bofferding1, Heidi Gildersleeve1 Margaret J. McMillin1,2, Anita E. Beck1,2, PhD MD and Michael J. Bamshad1,2,3, MD
1Department of Pediatrics, University of Washington, Seattle WA
2Seattle Children’s Hospital, Seattle, WA
3Department of Genome Sciences, University of Washington, Seattle WA
Introduction
Figure 1. Schematic of the contractile apparatus of skeletal
muscle. Grey text denotes the names of the protein subunits. Red
text corresponds to the gene screened which encodes the subunit.
Figure 3. Gene schematics, Electropherograms of Exon 17 of MYH3, and FSS pedigree. The
individual affected with FSS has a heterozygous mutation at c.2014C>T. DNA from additional family
members was unavailable for sequencing. Electropherograms identify DNA sequence for FSS mutation
and wild type allele at location c.2014.
Results
Abstract
Distal Arthrogryposis (DA) is a group of congenital disorders
characterized by contractures of distal limbs. The
incidence of multiple congenital contractures is one in
three thousand births. Individuals with DA are cognitively
normal. Previous studies have shown that mutations in
TNNT3, TNNI2, TPM2, and MYH3 collectively explain
roughly 30% SHS cases and nearly 95% of FSS cases. These
four genes each encode protein subunits of skeletal muscle
and are hypothesized to be involved in muscular
contraction. Mutations in TNNI2 and TNNT3 may interfere
with the binding of the troponin complex to the
tropomyosin filament and/or inhibit the conformational
change of the troponin complex necessary for muscle
contraction. Mutations in MYH3 may interfere with the
binding of the myosin head to actin filaments. Mutations in
TPM2 may interfere with the interaction between the
tropomyosin filament and the binding site for the myosin
head on the actin filament. However, the precise
mechanism by which mutations in these genes affect
muscle contraction is unknown.
In this study, TNNT3, TNNI2, TPM2, and MYH3 were
screened in 19 individuals who were categorized into three
phenotype groups: un-classified Distal Arthrogryposis (UN
DA) n=13, Sheldon-Hall syndrome (SHS) n=5, and Freeman-
Sheldon syndrome (FSS) n=1.
•DNA samples were collected from one individual
diagnosed with FSS, five individuals diagnosed with
SHS and thirteen individuals with UN DA.
•Primers were designed to capture each of the 9
exons of TPM2, exons 17 and 18 of MYH3, exon 10 of
TNNT3, and exon 8 of TNNI2 in all nineteen
individuals.
•Sanger sequencing was performed on each sample.
•Electropherograms of sequence reads were aligned
in Codon Code Aligner software.
•Mutations were determined by comparison to a
control DNA and a reference sequence from the
Ensembl database (GRCh37).
Affected female and male Unaffected female and male
Key
Distal Arthrogryposis (DA) is a group of syndromes defined by multiple congenital contractures, primarily of the limbs. DA is divided into
subtypes based on the presence of additional clinical features. DA1 is characterized by isolated contractures of the hands and feet.
Sheldon-Hall syndrome (SHS), also known as DA2B, involves mild facial contractures, small mouth and prominent nasolabial folds.
Freeman-Sheldon syndrome (FSS), also known as DA2A, is distinguished by severe facial contractures with pursed lips and H-shaped
dimpling of the chin. DA1, DA2A and DA2B are all autosomal dominant disorders. Mutations in at least four genes, TNNT3, TNNI2, TPM2,
and MYH3, have been shown to cause DA1 and DA2B, whereas DA2A has only been reported to have mutations in MYH3. Each of these
genes encodes a component of the contractile apparatus of skeletal muscle. We screened nineteen individuals diagnosed with DA2A,
DA2B, or an unclassified type of DA for mutations in TNNT3, TNNI2, TPM2, and MYH3. A missense mutation c.2014C>T (p.R672C) in exon
17 of MYH3 was identified in an individual with FSS. This mutation has been previously reported as pathogenic in individuals with FSS.
Parental DNA was unavailable for sequencing.
I.
II.
Pedigree of Individual with FSS
Exon 17 mutation c.2014C>T in MYH3
Al-Haggar, Mohammad. " CLINICAL BRIEF p.R672C Mutation of
MYH3 Gene in an Egyptian Infant Presented with Freeman-
Sheldon Syndrome." Indian Journal Pediatrics . 17 May
2010. academia.edu. 8 August
2012 <www.mansoura.academia.edu>.
MYH3. 30 July 2012 National Institute of Health. 8 August
2012 <http://ghr.nlm.nih.gov/gene/MYH3>.
myosin, heavy chain 3, skeletal muscle, embryonic. 15 May
2012 Weizmann Institute of Health. 8 August
2012 <http://www.genecards.org/cgi-
bin/carddisp.pl?gene=MYH3>.
Robinson, Paul . "Mutations in fast skeletal troponin I, troponin
T, and β-tropomyosin that cause distal arthrogryposis all
increase contractile function."
The FASEB Journal . 2006. 28 June
2012 <www.faseb.org/content/21/3/896.long>.
Toydemir, Reha. "Mutations in embryonic myosin heavy chain
(MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall
syndrome." Nature Genetics . 2006. 7 August
2012 <http://www.nature.com/ng/journal/v38/n5/full/ng177
Literature Cited
Acknowledgements
Special thanks to my mentor, Kathryn Bofferding, for
being incredibly patient and guiding me through my
research project. Thank you to Dr. Michael Bamshad (PI)
for granting me the opportunity to work and learn in the
lab. Also, thank you to everyone in the Bamshad lab and
to my lab mates for supporting and aiding me through my
research.
This research was supported by University of Washington
STAR Program (67-3473)
Conclusion
Figure 4. Protein
crystal structure of
MYH3. R672C,
underlined, indicates
the amino acid
position and the
predicted protein
consequence of the
c.2014C>T mutation.
•No mutations were identified in the sequenced exons of
TNNI2, TPM2, TNNT3 or MYH3 in any of the individuals
with UN DA or DA2B.
•It is possible that large-scale deletions or duplications,
which would not be detected in the sequence read, may
have occurred. Such deletions or duplications may be
detected by future research.
•Screening of additional exons, intronic and promoter
regions may also yield causative mutations.
•Re-sequencing of exon 1 of TPM2 may produce mutations
as exon 1 in all samples failed to sequence.
•In the one individual with a diagnosis of FSS, a mutation
was identified in exon 17 of MYH3. Since this mutation
has been previously reported in individuals with FSS, it is
likely that this mutation is pathogenic.
(TNNT3)
(TPM2)
(TNNI2)
(MYH3)
TPM2
TNNT3
TNNI2
MYH3
Gene Schematic Key
Sequenced Exon
Unsequenced Exon
Untranslated Region
A
Figure 2. Photos of FSS and SHS Phenotypes. A) Phenotype of classic Freeman-Sheldon B) Phenotype of
classic Sheldon-Hall C) and D) Muscular limb contractures characteristic of distal arthrogryposis syndromes.
C
D
B
R672C
c.2014C>T p.R672C
Wild Type
FSS
*These photos are to illustrate the phenotypes of FSS, SHS and limb contractures; they are not the individuals in this study.