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Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia.

Rios J, Stein E, Shendure J, Hobbs HH, Cohen JC - Hum. Mol. Genet. (2010)

Bottom Line: This finding indicated that the infant has sitosterolemia.Diagnosis was confirmed by the finding of severe sitosterolemia in a blood sample obtained after the infant had been weaned.These findings demonstrate that whole-genome (or exome) sequencing can be a valuable aid to diagnose genetic diseases, even in individual patients.

View Article: PubMed Central - PubMed

Affiliation: McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas,TX 75390, USA.

ABSTRACT
Whole-genome sequencing is a potentially powerful tool for the diagnosis of genetic diseases. Here, we used sequencing-by-ligation to sequence the genome of an 11-month-old breast-fed girl with xanthomas and very high plasma cholesterol levels (1023 mg/dl). Her parents had normal plasma cholesterol levels and reported no family history of hypercholesterolemia, suggesting either an autosomal recessive disorder or a de novo mutation. Known genetic causes of severe hypercholesterolemia were ruled out by sequencing the responsible genes (LDLRAP, LDLR, PCSK9, APOE and APOB), and sitosterolemia was ruled out by documenting a normal plasma sitosterol:cholesterol ratio. Sequencing revealed 3 797 207 deviations from the reference sequence, of which 9726 were nonsynonymous single-nucleotide substitutions. A total of 9027 of the nonsynonymous substitutions were present in dbSNP or in 21 additional individuals from whom complete exonic sequences were available. The 699 novel nonsynonymous substitutions were distributed among 604 genes, 23 of which were single-copy genes that each contained 2 nonsynonymous substitutions consistent with an autosomal recessive model. One gene, ABCG5, had two nonsense mutations (Q16X and R446X). This finding indicated that the infant has sitosterolemia. Thus, whole-genome sequencing led to the diagnosis of a known disease with an atypical presentation. Diagnosis was confirmed by the finding of severe sitosterolemia in a blood sample obtained after the infant had been weaned. These findings demonstrate that whole-genome (or exome) sequencing can be a valuable aid to diagnose genetic diseases, even in individual patients.

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Related in: MedlinePlus

Overview of the analysis of sequence variations identified by whole-genome sequencing. (A) The whole genome of the proband was sequenced by Complete Genomics, Inc., using a sequencing-by-ligation method as described (19). A total of 138 Gb of mappable sequence was obtained, for a mean fold coverage of 49×. (B) Confirmation of ABCG5 mutations in DNA samples from the mother and father of the proband.
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DDQ352F2: Overview of the analysis of sequence variations identified by whole-genome sequencing. (A) The whole genome of the proband was sequenced by Complete Genomics, Inc., using a sequencing-by-ligation method as described (19). A total of 138 Gb of mappable sequence was obtained, for a mean fold coverage of 49×. (B) Confirmation of ABCG5 mutations in DNA samples from the mother and father of the proband.

Mentions: To provide a more comprehensive screen for possible mutations causing the hypercholesterolemia in the child, whole-genome sequencing was performed by Complete Genomics, Inc. (Mountain View, CA, USA), using a sequencing-by-ligation method as described in detail previously (19). Sequencing of the proband's DNA sample yielded 138 gigabase (Gb) of mappable sequence, for an average fold coverage of 49× per base. A total of 3 797 207 deviations from the reference sequence were noted (Fig. 2A), of which 3 295 207 were single-nucleotide substitutions (including 2 245 981 heterozygous and 1 049 225 homozygous) and 502 000 were insertions, deletions or more complex rearrangements. Since most Mendelian disorders are caused by rare single-nucleotide substitutions in coding regions and exon splice junctions, we restricted our initial search to nonsynonymous variants and splice junction variants that were not present in the public repository of sequence variants (dbSNP) or in 16 exomes (2,20) and 5 genomes (J.C.C. and H.H.H., unpublished data) from 21 individuals who did not have hypercholesterolemia.Figure 2.


Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia.

Rios J, Stein E, Shendure J, Hobbs HH, Cohen JC - Hum. Mol. Genet. (2010)

Overview of the analysis of sequence variations identified by whole-genome sequencing. (A) The whole genome of the proband was sequenced by Complete Genomics, Inc., using a sequencing-by-ligation method as described (19). A total of 138 Gb of mappable sequence was obtained, for a mean fold coverage of 49×. (B) Confirmation of ABCG5 mutations in DNA samples from the mother and father of the proband.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2957323&req=5

DDQ352F2: Overview of the analysis of sequence variations identified by whole-genome sequencing. (A) The whole genome of the proband was sequenced by Complete Genomics, Inc., using a sequencing-by-ligation method as described (19). A total of 138 Gb of mappable sequence was obtained, for a mean fold coverage of 49×. (B) Confirmation of ABCG5 mutations in DNA samples from the mother and father of the proband.
Mentions: To provide a more comprehensive screen for possible mutations causing the hypercholesterolemia in the child, whole-genome sequencing was performed by Complete Genomics, Inc. (Mountain View, CA, USA), using a sequencing-by-ligation method as described in detail previously (19). Sequencing of the proband's DNA sample yielded 138 gigabase (Gb) of mappable sequence, for an average fold coverage of 49× per base. A total of 3 797 207 deviations from the reference sequence were noted (Fig. 2A), of which 3 295 207 were single-nucleotide substitutions (including 2 245 981 heterozygous and 1 049 225 homozygous) and 502 000 were insertions, deletions or more complex rearrangements. Since most Mendelian disorders are caused by rare single-nucleotide substitutions in coding regions and exon splice junctions, we restricted our initial search to nonsynonymous variants and splice junction variants that were not present in the public repository of sequence variants (dbSNP) or in 16 exomes (2,20) and 5 genomes (J.C.C. and H.H.H., unpublished data) from 21 individuals who did not have hypercholesterolemia.Figure 2.

Bottom Line: This finding indicated that the infant has sitosterolemia.Diagnosis was confirmed by the finding of severe sitosterolemia in a blood sample obtained after the infant had been weaned.These findings demonstrate that whole-genome (or exome) sequencing can be a valuable aid to diagnose genetic diseases, even in individual patients.

View Article: PubMed Central - PubMed

Affiliation: McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas,TX 75390, USA.

ABSTRACT
Whole-genome sequencing is a potentially powerful tool for the diagnosis of genetic diseases. Here, we used sequencing-by-ligation to sequence the genome of an 11-month-old breast-fed girl with xanthomas and very high plasma cholesterol levels (1023 mg/dl). Her parents had normal plasma cholesterol levels and reported no family history of hypercholesterolemia, suggesting either an autosomal recessive disorder or a de novo mutation. Known genetic causes of severe hypercholesterolemia were ruled out by sequencing the responsible genes (LDLRAP, LDLR, PCSK9, APOE and APOB), and sitosterolemia was ruled out by documenting a normal plasma sitosterol:cholesterol ratio. Sequencing revealed 3 797 207 deviations from the reference sequence, of which 9726 were nonsynonymous single-nucleotide substitutions. A total of 9027 of the nonsynonymous substitutions were present in dbSNP or in 21 additional individuals from whom complete exonic sequences were available. The 699 novel nonsynonymous substitutions were distributed among 604 genes, 23 of which were single-copy genes that each contained 2 nonsynonymous substitutions consistent with an autosomal recessive model. One gene, ABCG5, had two nonsense mutations (Q16X and R446X). This finding indicated that the infant has sitosterolemia. Thus, whole-genome sequencing led to the diagnosis of a known disease with an atypical presentation. Diagnosis was confirmed by the finding of severe sitosterolemia in a blood sample obtained after the infant had been weaned. These findings demonstrate that whole-genome (or exome) sequencing can be a valuable aid to diagnose genetic diseases, even in individual patients.

Show MeSH
Related in: MedlinePlus