Case study
DNA from saliva offers clues to genetic disorders
Dr. Naomichi Matsumoto
Department of Human Genetics, Yokohama City University Graduate School of Medicine

Study overview
Dr. Naomichi Matsumoto and his team at Yokohama City University’s Departmentof Human Genetics are currently involved in a 3 year project researching genetic
diseases, including mendelian disorders. Genetic diseases are caused by a single
mutation in the structure of DNA, which results in a single defect with pathologic
consequences. More than 4,000 human diseases are caused by single gene defects
such as sickle-cell anemia, Tay-Sachs disease and cystic fibrosis. Genetic diseases
rarely have effective treatments available. Dr. Matsumoto has been involved indisease-related genome analysis for many years and has seen significant technology
advances (exome and Next Generation Sequencing) that will facilitate improved
accuracy for gene mutation analysis. It is important to identify the genes responsible
for these diseases in individuals and carriers for whom genetic testing and counsellingare critical. Dr. Matsumoto plans to analyze 1,000 DNA samples collected from
affected individuals and family members over the 3 year period of the study.

Oragene device
prior to collection

Main challenges

Sample ready fortransport, storage
and processing

Affected patients require regular hospital visits and blood draws for comprehensive
testing. However, research into genetic disease also requires DNA from family
members of the patient. Therefore, the main challenges faced by the research team
were collecting samples from family members of affected individuals who did notaccompany the patient to the hospital. In addition, the DNA quality had to meetthe requirements for PCR sequencing of candidate genes as well as the more
stringent requirements of exome sequencing (both the Agilent SureSelect and theIllumina® HiSeq™ 2000 are used for this study). The DNA collection method had
to be cost-effective to fall within strict budget guidelines for the project.

Collection methods considered
In addition to whole blood, Dr. Matsumoto looked for alternatives that would
facilitate self-collection of DNA samples while meeting the quality standards forhis downstream analysis. Oragene®/saliva collection kits were the primary method
considered as an alternative to blood sample collection.

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Superior samples
Proven performanceWhy Oragene/saliva collection kits?
Dr. Matsumoto had used Oragene/saliva collection kits for a previous research
project1. Based on this experience, he knew the product would meet his requirements
for DNA quality and offer a convenient self-collection method for family members.
The Oragene kits can also be transported via the standard postal service, facilitating
easy and rapid return of the collected sample to the research team for analysis.
Oragene offered convenience and increased access to family members.

Results
The Oragene/saliva collection kits are helping Dr. Matsumoto achieve a greaterthan 95% compliance rate for his study while meeting the requirement for
PCR-direct sequencing and even Next Generation Sequencing, when it is required(see Table 1). The data he obtained from the analysis of samples is comparable forresults achieved using blood (see Table 2). The data obtained from the samples
has already helped him identify culprit mutations in several mendelian diseases
including: Coffin-Siris syndrome, spinocerebellar ataxia, HCAHC, early infantile
epileptic encephalopathy and more.
Table 1DNA ID

After purification

Sample ID

Concentration(ng/µL)

Total amount(ng)

A260/A280

A260/A230

dsDNA concentration(ng/µL)1362.9

18145

1.90

2.03

89.2

2368.1

18405

1.91

1.84

97.4

3394.7

19735

1.94

1.89

58.8

4

234.2

11710

1.86

2.00

40.7

5324.2

16210

1.89

1.83

62.3

Measured by Nanodrop
Measured by Qubit (Invitrogen system)
Table 2Sample
ID

Total
outputMean
depth

Percent bases Percent bases Percent bases Percent aligned
above 5above 10above 20
to genome

14200958785

125.51

96

94.5

90.6

97.01446718

23722946669

111.23

95.7

93.9

89.3

97.39562778

34384176351

130.98

95.9

94.5

90.8

95.30240887

43690525897

110.26

95.7

94

89.4

96.83854435

53720171081

111.14

95.7

94.1

89.6

96.95681714

1 Yoneda Y., Haginoya K., Arai H., Yamaoka S., Tsurusaki Y., Doi H., Miyake N., (...), Saitsu H. De novo and inherited mutations inCOL4A2, encoding the type IV collagen α2 chain cause porencephaly (2012) American Journal of Human Genetics, 90 (1), pp. 86-90.
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Superior samples • Proven performance
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