Diabetes Metab J.  2015 Oct;39(5):439-443. 10.4093/dmj.2015.39.5.439.

Identification of Two Cases of Ciliopathy-Associated Diabetes and Their Mutation Analysis Using Whole Exome Sequencing

• Kim MK
• Kwak SH
• Kang S
• Jung HS
• Cho YM
• Kim SY
• Park KS

• KMID: 2174018
• DOI: http://doi.org/10.4093/dmj.2015.39.5.439

Abstract

BACKGROUND
Alstrom syndrome and Bardet-Biedl syndrome are autosomal recessively inherited ciliopathies with common characteristics of obesity, diabetes, and blindness. Alstrom syndrome is caused by a mutation in the ALMS1 gene, and Bardet-Biedl syndrome is caused by mutations in BBS1-16 genes. Herein we report genetically confirmed cases of Alstrom syndrome and Bardet-Biedl syndrome in Korea using whole exome sequencing.
METHODS
Exome capture was done using SureSelect Human All Exon Kit V4+UTRs (Agilent Technologies). HiSeq2000 system (Illumina) was used for massive parallel sequencing. Sanger sequencing was used for genotype confirmation and familial cosegregation analysis.
RESULTS
A 21-year old Korean woman was clinically diagnosed with Alstrom syndrome. She had diabetes, blindness, obesity, severe insulin resistance, and hearing loss. Whole exome sequencing revealed a nonsense mutation in exon 10 of ALMS1 (c.8776C>T, p.R2926X) and a seven base-pair deletion resulting in frameshift mutation in exon 8 (c.6410_6416del, p.2137_2139del). A 24-year-old Korean man had Bardet-Biedl syndrome with diabetes, blindness, obesity, and a history of polydactyly. Whole exome sequencing revealed a nonsynonymous mutation in exon 11 of the BBS1 gene (c.1061A>G, p.E354G) and mutation at the normal splicing recognition site of exon 7 of the BBS1 gene (c.519-1G>T).
CONCLUSION
We found novel compound heterozygous mutations of Alstrom syndrome and Bardet-Biedl syndrome using whole exome sequencing. The whole exome sequencing successfully identified novel genetic variants of ciliopathy-associated diabetes.

Keyword

ALMS1; Alstrom syndrome; Bardet-Biedl syndrome; BBS1; Ciliopathy; Diabetes mellitus; Next generation sequencing; Sanger sequencing; Whole exome sequencing

MeSH Terms

Alstrom Syndrome
Bardet-Biedl Syndrome
Blindness
Codon, Nonsense
Diabetes Mellitus
Exome*
Exons
Female
Frameshift Mutation
Genotype
Hearing Loss
Humans
Insulin Resistance
Korea
Obesity
Obesity, Morbid
Polydactyly
Young Adult
Codon, Nonsense

Figure

• 

  Fig. 1 Pedigrees of Alström syndrome and Bardet-Biedl syndrome patients. (A) The Alström syndrome patient had compound heterozygous mutations in the ALMS1 gene. A mutation in exon 10 of the ALMS1 gene (c.8776C>T, p.R2926X), which introduced a stop codon, was maternally inherited, and a seven base pair deletion in exon 8 of ALMS1 gene mutation (c.6410_6416del, p.2137_2139del) might have been inherited from the patient's father or newly introduced as a de novo mutation. (B) The Bardet-Biedl syndrome patient also had a compound heterozygous mutation. A mutation at a normal splicing recognition site of exon 7 on the BBS1 gene (c.519-1G>T) was maternally inherited, and a novel nonsynonymous mutation in exon 11 of BBS1 gene (c.1061A>G, p.E354G) was paternally inherited. Circles, females; squares, males; filled symbols indicate affected members; empty symbols indicate healthy family members; symbols with dots in the center indicate obligate carriers; slashed symbols indicate those who had previously died. The DNA sequence electropherograms are shown for the reference (top) and subject (bottom). The sequences were analyzed using Variant Reporter v.1.1 (Applied Biosystems) with IUPAC (The International Union of Pure and Applied Chemistry) codes. WT, wild type.

Reference

1. Hildebrandt F, Benzing T, Katsanis N. Ciliopathies. N Engl J Med. 2011; 364:1533–1543.

2. Lee JE, Gleeson JG. A systems-biology approach to understanding the ciliopathy disorders. Genome Med. 2011; 3:59.

3. Girard D, Petrovsky N. Alstrom syndrome: insights into the pathogenesis of metabolic disorders. Nat Rev Endocrinol. 2011; 7:77–88.

4. Forsythe E, Beales PL. Bardet-Biedl syndrome. Eur J Hum Genet. 2013; 21:8–13.

5. Marshall JD, Maffei P, Beck S, Barrett TG, Paisey R, Naggert JK. Clinical utility gene card for: Alstrom syndrome update 2013. Eur J Hum Genet. 2013; 21.

6. Slavotinek A, Beales P. Clinical utility gene card for: Bardet-Biedl syndrome. Eur J Hum Genet. 2011; 19.

7. Aliferis K, Helle S, Gyapay G, Duchatelet S, Stoetzel C, Mandel JL, Dollfus H. Differentiating Alstrom from Bardet-Biedl syndrome (BBS) using systematic ciliopathy genes sequencing. Ophthalmic Genet. 2012; 33:18–22.

8. Chen J, Smaoui N, Hammer MB, Jiao X, Riazuddin SA, Harper S, Katsanis N, Riazuddin S, Chaabouni H, Berson EL, Hejtmancik JF. Molecular analysis of Bardet-Biedl syndrome families: report of 21 novel mutations in 10 genes. Invest Ophthalmol Vis Sci. 2011; 52:5317–5324.

9. Goh G, Choi M. Application of whole exome sequencing to identify disease-causing variants in inherited human diseases. Genomics Inform. 2012; 10:214–219.

10. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25:1754–1760.

11. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20:1297–1303.

12. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010; 7:248–249.

13. Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. 2013; Chapter 7:Unit7.20.

14. Marshall JD, Hinman EG, Collin GB, Beck S, Cerqueira R, Maffei P, Milan G, Zhang W, Wilson DI, Hearn T, Tavares P, Vettor R, Veronese C, Martin M, So WV, Nishina PM, Naggert JK. Spectrum of ALMS1 variants and evaluation of genotype-phenotype correlations in Alstrom syndrome. Hum Mutat. 2007; 28:1114–1123.

15. Yoon KH, Son HY, Kang SK, Choi YH, Cha BY, Cho HS, Kim KB, Kang JH, Choo YM, Bae SS. A case of Alstrom syndrome. J Korean Soc Endocrinol. 1998; 13:501–508.

16. Daniels AB, Sandberg MA, Chen J, Weigel-DiFranco C, Fielding Hejtmancic J, Berson EL. Genotype-phenotype correlations in Bardet-Biedl syndrome. Arch Ophthalmol. 2012; 130:901–907.

17. Yoon SC, Lee HJ, Ko JM, Kang HG, Cheong HI, Yu HG, Kim JH. Two siblings with Bardet-Biedl syndrome caused by mutations in BBS10: the first case identified in Korea. J Genet Med. 2014; 11:31–35.

18. Collins FS, Hamburg MA. First FDA authorization for next-generation sequencer. N Engl J Med. 2013; 369:2369–2371.