Mapping Genes for SLE:A Paradigm for Human Disease?

Stephen S. Rich, Ph.D.

Department of Public Health Sciences

Wake Forest University School of Medicine

Simple vs Complex Traits

Simple Traits

-rare

-single gene (Mendelian)

-severe mutations

-large phenotypic effect

Complex Traits

-common

-many genes (Oligogenic)

-mild mutations

-small phenotypic effect

Complex trait mapping is the major challenge in human genetics

Difficulties in Complex Disease

• Identifying genes that contribute to susceptibility of complex disease difficult due to underlying biological mechanisms– Phenotypic heterogeneity– Genetic heterogeneity– Gene-environment interaction

• Limited study power to detect small effect susceptibility genes (QTLs)

• Available sample size for genetic studies

Gene - Environment Interaction

Gene - Environment Interaction:Complex Genetic Diseases

Genetic/Host Susceptibility

Presymptomatic Conditions

(Risk Factors or Markers of Disease

Susceptibility)Environmental

Influences

Symptomatic Disease (Reversible or Irreversible Changes in Organ

Structure and Function)

Steps Towards Finding a Gene

• Identification of a population

• Clinical assessment

• Linkage analysis - genome screen

• Fine mapping and gene localization

• Gene identification / sequence variants

• Functional genomics: Gene expression

Issues in Clinical Assessment• Disease phenotype definitions

– medical history, evidence of sub-clinical outcome, and a confirmation through a clinical examination

– outpatient clinic records with varying data

– positive answer to the questions • “Have you ever been diagnosed with ...?” and • “If yes, has this happened more than once?”

• Standardized questionnaires• Standardized protocols• Study coordination and training of staff• Quality Control / Quality Assurance

Choices of a Population

• Representation– Isolated, admixed or inbred – Mixed, heterogeneous populations

• Family structure– Unrelated individuals– Families

• Parents and children • Extended families (pedigrees)

• Source– Single ethnic group– Multiple ethnic groups

Example of Linkage Analysis

D1S218

D1S158

D1S444

D1S218

D1S158

D1S444

D1S218

D1S158

D1S444

Affected Sib Pair Family

a//b c//d

a//c 25% a//c50% a//d or b//c25% b//d

Systemic Lupus Erythematosus• SLE is a chronic autoimmune inflammatory disease

characterized by the production of pathogenic autoantibodies

• SLE is a clinically heterogeneous disease that affects a variety of organs such as joints, skin, blood and kidneys

• SLE disproportionately affects women (>90%) of child-bearing age

• Prevalence of SLE in the United States is estimated to be between 40 - 45 cases per 100,000 (Hochberg 1997)

Familiality of SLE• SLE has a strong genetic component

– Increased concordance rates among MZ twins

(Deapen et al., 1992, Reichlin et al., 1992)

– Increased risk to siblings (S=10-20; Vyse and Todd, 1996)

• SLE does not exhibit simple Mendelian inheritance patterns and may involve – incomplete penetrance

– phenocopies

– genetic heterogeneity

– polygenic inheritance

– modifying environmental effects

Affected Relative Pair Collections

• Minnesota cohort– 187 SLE sib pair families– 6p11-21, 16q13, 14q21-23, 20p12.3

• Oklahoma cohort– 94 extended multiplex pedigrees– 1q23, 13q32, 20q13, 1q31

• Ethnic-specific effects

NPL Regression Analysis of Combined Genome Scan for SLE

Chromosomal LOD-1 Region Nearest Marker LOD Interval

Chr 1 @ 263 D1S2785 2.14 253-285

Chr 4 @ 21 D4S403 3.65 11-28

Chr 4 @ 165 D4S2368 2.00 147-178

Chr 6 @ 68 D6S2410 4.90 61-80

Chr 6 @ 85 D6S1031 3.84 57-100

Chr 7 @ 27 D7S507 2.47 6-37

Chr 16 @ 77 D16S3253/D16S503 3.51 65-85

Chr 20 @ 62 D20S481/D20S119 1.97 57-67

Combined Genome Scan for SLESample Similarities and Differences

Chromosomal LOD Score

Region Nearest Marker Combined MN OK

Chr 1 @ 263 D1S2785 2.14 2.2 0.3

Chr 4 @ 21 D4S403 3.65 1.8 1.9

Chr 4 @ 165 D4S2368 2.00 1.9 0.3

Chr 6 @ 68 D6S2410 4.90 4.3 1.0

Chr 6 @ 85 D6S1031 3.84 3.6 0.7

Chr 7 @ 27 D7S507 2.47 1.5 1.0

Chr 16 @ 77 D16S3253/D16S503 3.51 4.3 0.3

Chr 20 @ 62 D20S481/D20S119 1.97 2.0 0.3

Combined Genome Scan for SLEEthnic Differences

LOD Score

Chromosomal African

Region Nearest Marker Combined American Caucasian

Chr 1 @ 263 D1S2785 2.14 0.0 1.8

Chr 4 @ 21 D4S403 3.65 0.0 4.5

Chr 4 @ 165 D4S2368 2.00 0.7 1.9

Chr 6 @ 68 D6S2410 4.90 1.6 2.6

Chr 6 @ 85 D6S1031 3.84 2.5 1.4

Chr 7 @ 27 D7S507 2.47 0.0 2.9

Chr 16 @ 77 D16S3253/D16S503 3.51 0.1 3.2

Chr 20 @ 62 D20S481/D20S119 1.97 0.0 2.7

SummaryThe Lupus SCOR combined genome scan for SLE provides evidence of linkage to several chromosomal regions: 1q, 4p, 4q, 6, 7p, 16, 20

With the exception of chromosome 6, our linkage peaks tend to be dominated by the Caucasian pedigrees in our sample

Several of our linkage signals appear to be supported by published genome scans

Fine mapping efforts related to these linkage regions are underway within the SCOR as part of its mission to map and clone genes predisposing to SLE and related phenotypes

Genetic

Mapping

Fine

Mapping

Susceptibility

Gene(s) ACGCCACC

ACGTCACC

DNA

Phenotypes

Diagnostic Tests

New Mechanisms

New Drugs

Gene-Environment Interactions

Genome Screening

and Linkage Analyses

Positional Cloning in Complex Diseases

Acknowledgements

University of Alabama-Birmingham

Robert P. Kimberly

Jeffrey C. Edberg

University of Minnesota

Timothy W. Behrens

Patrick M. Gaffney

Robert R. Graham

University of Oklahoma

John B. Harley

Jennifer H. Kelly

Courtney Gray-McGuire

Kathy L. Moser*

Wake Forest University

Stephen S. Rich

W. Mark Brown

Carl D. Langefeld