Genetic Analysis in Human DiseaseNataly Manjarrez, PhD

GENETIC ANALYSIS IN HUMAN DISEASENataly Manjarrez Orduño, PhDAssistant Investigator,Feinstein Institute for Medical Researchnmanjarrez@nshs.edu

Outline

• Intro and genetics vocabulary.• Single & polygenic genetic

disorders.• Omics in the clinical practice.• Outlook

Aim

• Talk and understand genetics.• Understand quality control in

publications.• Incorporate it to practice.

Your patients may be talking genetics already.

Genetic diseases in pediatrics

Genetic disorders and birth defects account for ~12% of pediatric admissions in the US.

There are around 7000 rare diseases identified in the US, with 80% of genetic origin.

30% of rare disease patients die before the age of 5.

It is all about DNA

Owald T. Avery MD, Colin McCLeod MD, Macylin McCarty

MD

Studies on the Chemical Nature of the Substance Inducing

Transformation of Pneumococcal Types: Induction

of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III

J. Exp Med, 1944

Genome

Locus/Loci

SNP

Common Genetic TermsGenotype: An individual’s genetic makeup - forms of a particular gene at a given locusPhenotype: The observable expression of a genotype Allele: one of the forms of the same gene/locus/SNP.Homozygous: Identical forms of a particular geneHeterozygous: Different forms of a gene– CARRIER if one normal and one abnormal.

Dominant: Condition phenotypically expressed in someone carrying one copy of a mutant gene

Recessive: Condition phenotypically expressed only in someone with two copies of the mutant gene.

Carrier: has recessive gene but no disease.

Expressivity: Qualitative characteristic trait expressed in various ways.

Penetrance: Quantitative characteristic degree or severity of the abnormality

Family History

• Reflects the consequences of genetic susceptibilities, shared environment and common behaviors.

• Allows us to identify potentially inherited disorders in families.

• Is an independent risk factor for most chronic diseases of public health significance.In this day and age, family history is still one of the strongest

genetic tools.

Common Genetic Terms

What if “Attached earlobes” this is a disease?

Is Ee completely healthy (carrier) or is there a degree of Expressivity?

Does everyone with ee gets the disease? What about penetrance?

Male / boy

Female / girl

Pregnancy loss.Include number of weeks, if known.

The diagonal line is used to show that the person has died.

Adopted

8

What if there is limited information about family members?•If you do not know names and ages of familymembers, but do know the number of boys andthe number of girls, you can do this:

•If you do not know the number of boysand the number of girls, use diamond with number inside it (if total is known) or “?”.

Example: This shows that there are 8 children.

5 3Example: This shows that there

are 5 boys and 3 girls.

This line is used to show parents who are divorced/not together

SB

SB standsfor stillbirth.Include number of weeks, if known.

Single Gene Traits/Disorders

• Traits that are determined by one particular gene– Characterized by their transmission

pattern in families – PEDIGREE ANALYSIS.

– Able to determine risks for particular family members if know mode of inheritance

Autosomal Dominant Diseases

• Physically expressed if only one copy of gene is present.

• An affected parent has a 50% chance of passing the gene to a child.

• Some are due to new mutations.

Autosomal Recessive Diseases

• Physically expressed only if both chromosomes carry a copy of the gene

Rare diseases may fall mostly in this category.

X-linked inheritance

Chromosomal disorders

Genetics of complex traits and disease

The spectrum of genetic effects in complex diseases

Disease Causation: The Big Picture

Phenotype

Genotype Environment

Chance/Fate

If we think a disease or trait has a genetic component, how

can we find identify the relevant genetic variation?

SNP diversity between any two unrelated individuals:

~ 3 million base pairs

Human Genetic Variation, NIH

Association in population samples

Affecteds Controls

Where effects are probabilistic, must measure frequency in affected and control

populations

Most of the genome does not encode genes

It is a matter of probability.

1978 1987 2003 2004 2005 2007 2008 2009 2010

HLA-DR4

HLA “shared epitope”

hypothesis PADI4 PTPN22 CTLA4

TNFAIP3STAT4TRAF1/C5IL2-IL21

CD40CCl21CD244PIP4K2CIL2RAPRKCQIL2RBAFF3TNFRSF14

RELBLKTAGAPCD28TRAF6PTPRCFCGR2APRDM1CD2/CD58

SIAESPRED2RBPJCCR6IRF5PXKIL6S

Lots of genes/genetic regions discovered for autoimmune disease – most in the last 3-4 years using genome wide association studies (GWAS)

Timeline for discovery in rheumatoid arthritis

The strength of each genetic association is modest, generally odds ratios <2 (with exception of HLA)

Top GWAS hits in T1 diabetes Concannon, Rich, Nepom Genetics of Type 1A Diabetes N Engl J Med 2009;360:1646-54.

GWAS – where are the hits?

• 3800 SNPs identified for 427 diseases and traits

• Only 7% in coding regions• >50% in DNAse sensitive

sites, presumed regulatory regions

Science 232:1031, 2011Stamatoyannopoulos, Cold Spring Harbor, May 2011

Genotyping, not sequencing!

Omics and medicine

Genome:

Epigenome

Transcriptome:

Microbiome:

• Whole genome sequencing• Exome sequencing.

• Analysis of the “marks” in the DNA

• RNA sequencing.

• Sequencing for microorganism ID.

Genomes, genomes

• First genome

$2,700,000,00015 years,

• Current

$5,000One week

Whole vs exome sequencing

Whole genome sequencing

• Reserved for individuals in whom

– the likelihood of success is high – reasonable clinical testing has not

achieved answer– molecular diagnosis has the

potential to advance clinical decision making

The omics landscape

Modified from Genome Res, 2009 19:521-532.

Rare and orphan diseases

• > 5,000 monogenic disorders have been identified with more being discovered.

• Most humans have about 6-8 defective genes, most being recessive & therefore not expressed.

• Sequencing might help to uncover not only the cause of a disorder but also other potential mutations.

The real picture

Sci Transl Med 3, 87re3 (2011);

FAMILY HISTORY!!!

Genetics and the future of medicine

• Complete definition of genetic variation of individuals at reasonable cost is only a few years away

• The interpretation of these data are going to be major challenge

• Large populations need to be studied to connect phenotypic/disease state to genetic variation

• Regulatory variation in the genome (ENCODE project) is going to be key to understanding

• Data mining in the context of large health will be crucial to the success of this effort