1

Michael German, MDUCSF Diabetes Center

Exome Sequencingand the

Genetics of Diabetes

Age-Adjusted Prevalence of Diagnosed Diabetes Among US Adults

<4.5% Missing data 4.5%–5.9% 6.0%–7.4% 7.5%–8.9% ≥9.0%

CDC’s Division of Diabetes Translation. National Diabetes Surveillance System available at http://www.cdc.gov/diabetes/statistics

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013

2

CDC’s Division of Diabetes Translation. National Diabetes Surveillance System available at http://www.cdc.gov/diabetes/statistics

Number and Percentage of U.S. Population with Diagnosed Diabetes, 1958-2013

Diabetes in the US

3

Diabetes: GeneticsConcordance Rates in Identical Twins:

Type 1 Diabetes: ~40%.

Type 2 Diabetes: ~90%.

Type 1 Diabetes Genes1.  MHC Locus >50% of genetic risk

4

Type 1 Diabetes Genes1.  MHC Locus >50% of genetic risk2.  Insulin Gene

Type 1 Diabetes Genes1.  MHC Locus >50% of genetic risk2.  Insulin Gene3.  Others

Mehers, K. L. et al. Br Med Bull 2008 88:115-129; doi:10.1093/bmb/ldn045

5

Type 2 Diabetes:The Search for Genes

• Although type 2 diabetes runs in families, the inheritance in most families is complex.

• Currently, family history remains the most valuable genetic test.

Types of Diabetes

German, M.S., and Masharani, U. (2011). Pancreatic Hormones and Diabetes Mellitus. In Greenspan's Basic & Clinical Endocrinology. D.G. Gardner, D.M. Shoback, and F.S. Greenspan, eds. (New York: McGraw-Hill Medical), pp. 573-655.

6

Types of Diabetes

1.  Type 1 diabetes.

2.  Type 2 diabetes.

3.  Monogenic Diabetes.

4.  Secondary Diabetes.

5.  Gestational Diabetes (GDM).

1/200

1/12

1/200

1/200

1/6 pregnancies

Diabetes: GeneticsMonogenic Diabetes

•  Maturity Onset Diabetes of the Young (MODY)

•  Neonatal Diabetes (TNDM & PNDM)•  Mitochondrial Diabetes•  Rare forms of severe insulin resistance•  Syndromic Diabetes

7

MODY: Maturity Onset Diabetes of the Young

• Autosomal dominant inheritance pattern. --Every generation, 50%• Onset commonly before age 25.

• Not obese.•  Islet autoantibodies negative.

MODY2: GCK Glucokinase

• Combined β-cell and liver defect.Impaired insulin secretion in response to glucose.

• Moderate hyperglycemia.• No disease progression.•  Low incidence of complications.

8

MODY3: HNF1A/TCF1

RNApolymerase

HNF1A

MODY3: HNF1A•  β-cell defect.

Impaired insulin secretion.

• Severe hyperglycemia.• Disease progression.• High incidence of complications.• Very sensitive to sulfonylureas.•  Low renal glucose threshold.

9

MODY Genes

MODY1: HNF4AMODY2: GCKMODY3: HNF1A / TCF1

MODY5: HNF1B / TCF2

MODY5: HNF1B•  β-cell defect.

Impaired insulin secretion.•  Severe hyperglycemia.•  Disease progression.•  High incidence of complications.•  Congenital renal defects.•  Hypomagnesemia.•  Hypoplastic pancreas.•  Rarely presents as Neonatal Diabetes.

10

MODY GenesMODY1: HNF4AMODY2: GCKMODY3: HNF1A / TCF1MODY4: PDX1 / IPF1MODY5: HNF1B / TCF2MODY6: NEUROD1MODY7: KLF11

MODY GenesMODY1: HNF4AMODY2: GCKMODY3: HNF1A / TCF1MODY4: PDX1 / IPF1MODY5: HNF1B / TCF2MODY6: NEUROD1MODY7: KLF11MODY8: CELMODY9: PAX4MODY10: INSMODY11: BLK

11

Diabetes: Genetics

Neonatal Diabetes

•  Onset before age 6 months.•  TNDM Transient (<1 year). •  PNDM Permanent.

Neonatal DiabetesTransient: 6q24 (paternal isodisomy)Transient: ZFP57 (recessive)Trans/Perm: KCNJ11/Kir6.2 (activating/dominant)Trans/Perm: ABCC8/SUR1 (activating/dominant)Permanent: GATA6, GLIS3, MNX1, NEUROD1, NEUROG3, NKX2.2, PAX6, PDX1 / IPF1, PTF1, RFX6 (recessive)Permanent: GCK (recessive)Permanent: EIF2AK3/PERK (recessive)Permanent: INS (dominant)Autoimmune: FoxP3 (X-linked recessive)

Syndromic

12

Neonatal Diabetes

Aguilar-Bryan, L. et al. Endocr Rev 2008;29:265-291

Mitochondrial Diabetes• Maternally inherited• Non-obese• Insulin deficiency• Associated with deafness and other neural defects• Caused by mutations in the mitochondrial genome

13

Severe insulin Resistance

INSR (Insulin signaling)AKT2 (Insulin signaling)LMNA (Lipodystrophy)LMNB2 (Lipodystrophy)AGPAT2 (Lipodystrophy)BSCL2 (Lipodystrophy)PPARG (Lipodystrophy)

Syndromic Diabetes•  Chromosomal defects: Down's,

Klinefelter's, and Turner's syndromes.•  Neuromuscular syndromes: Friedreich's

ataxia, Huntington's chorea, Myotonic dystrophy, porphyria, others.

•  Obesity syndromes: Laurence-Moon-Biedl, Bardet-Biedl and Preder-Willi syndromes, others.

•  Wolfram's syndrome.•  Thiamine Responsive Megloblastic Anemia. •  Polyautommune syndromes: APS1, IPEX.

14

Clinical Approach to Genetic Forms of Diabetes

•  Why perform genetic tests?•  Identifies family members at risk. •  Provides information regarding natural

history, outcomes.•  Can alter management.•  What test do you do?•  Depends on pretest probability, costs,

insurance.

Exome Sequencing

15

Prior Probability of Specific Clinical Diagnosis

Specific Gene Testing

Whole Exome/Genome

Gene Panels

Low High

Locu

s H

eter

ogen

eity

Unknown

Large and Known

Limitedand

Known

Exome Sequencing•  Originally a research tool.•  Now a CLIA approved test. •  Available through UCSF Diabetes and

Clinical Genetics (UCSF/UCLA).•  Requires input from an experienced

geneticist.•  Cannot identify with certainty all variants.•  Effective when gene specific tests not

available or negative.

16

Onset Neonatal

Patients with Monogenic Diabetes

TNDM6q24KATP genes

PNDMSyndromic Gene specificNonsyndromic KATP genes INS, GCK

Later

Inheritance

MaternalMitochondrial sequence

Autosomal Recessive

Autosomal Dominant

SyndromicGene specific

MODYSyndromic Gene specific HNF1B, CELNonsyndromic

EuropeansMild? = GCKSevere? = HNF1A

Non-Europeans Gene panel, ExomeNegative?

AutoimmuneAutoimmune genes

Ins ResistantResistance genes

Exome

German Lab SupportHillblom Islet Genesis Network

(Larry L. Hillblom Foundation)Nora Eccles Treadwell FoundationHelmsley Trust

Bruce BradenJuvenile Diabetes Research FoundationAmerican Diabetes Association

NIH/NIDDK, UCSF DRC

17

References

• Bamshad, M.J., Ng, S.B., Bigham, A.W., Tabor, H.K., Emond, M.J., Nickerson, D.A., and Shendure, J. (2011). Exome sequencing as a tool for mendelian disease gene discovery. Nat Rev Genet 12, 745-755.• Doria, A., Patti, M.E., and Kahn, C.R. (2008). The emerging genetic architecture of type 2 diabetes. Cell Metab 8, 186-200.• Florez, J.C. (2008). Newly identified loci highlight beta cell dysfunction as a key cause of type 2 diabetes: where are the insulin resistance genes? Diabetologia 51, 1100-1110.• Greeley, S. A. W., Naylor, R. N., Philipson, L. H., & Bell, G. I. (2011). Neonatal Diabetes: An Expanding List of Genes Allows for Improved Diagnosis and Treatment. Current Diabetes Reports, 11(6), 519–532. doi:10.1007/s11892-011-0234-7.• McCarthy, M.I., and Zeggini, E. (2009). Genome-wide association studies in type 2 diabetes. Curr Diab Rep 9, 164-171.

References

• Mehers, K.L., and Gillespie, K.M. (2008). The genetic basis for type 1 diabetes. Br Med Bull 88, 115-129.• Roach, J.C., Glusman, G., Smit, A.F., Huff, C.D., Hubley, R., Shannon, P.T., Rowen, L., Pant, K.P., Goodman, N., Bamshad, M., Shendure, J., Drmanac, R., Jorde, L.B., Hood, L., and Galas, D.J. Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing. Science.• Schwitzgebel, V.M. (2014). Many faces of monogenic diabetes. Journal of Diabetes Investigation 5, 121-133. Dickson, S.P., Wang, K., Krantz, I., Hakonarson, H., and Goldstein, D.B. Rare variants create synthetic genome-wide associations. PLoS Biol 8, e1000294.• Vaxillaire, M., and Froguel, P. (2008). Monogenic diabetes in the young, pharmacogenetics and relevance to multifactorial forms of type 2 diabetes. Endocr Rev 29, 254-264.