SNP Analysis | Hokkaido System Science Co.,Ltd.

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Service Description

Description

In this service, PCR product is sequenced by Direct Sequence method, and the result is compared with the provided reference sequence to detect the SNP location. The result will be reported together with the waveform chart.

Service contents

	Please provide;
	-Purified PCR product of more than 20µL per analysis which were prepared as more than 10ng/µl
	-Sequence primers (Forward, Reverse)
	-Target gene information (reference sequence, known mutation information *1)
	*1 To send reference sequence and known mutation information, click here
	*The pretreatment for the analysis (purification of PCR product, gene amplification, primer design, primer synthesis, etc.) can be provided with separate fee as options if required. Please ask for detail.

	Basic content
	Sequence reaction Double Strand analysis using the Forward and Reverse primers

	Data analysis Waveform data is evaluated its accuracy using the dedicated software, and the SNP location is detected by comparing with the reference sequence.

	Result report Waveform data, sequence data and SNP location will be reported.

	Data analysis
	•	The provided PCR product sample will be analyzed by single extension sequence. The result of the detailed analysis with the dedicated software will be reported.
	•	The use of "SeqScape^® Software" by Applied Biosystems and its optimized basecalling algorithms which can show Quality Values enables highly accurate analysis.

	Domestic Lead Time For 20-96 sequence analysis : Two (2) weeks or more
	•	Sequence analysis generally includes two analyses using Forward and Reverse Primers for one comparison.

Cautions

•	Please note that we do not accept microorganisms, which do or may possess pathogenicity, or which are isolated from clinical samples or animals.
•	Samples will be accepted only when submitted in the form of DNA. Biological samples such as blood will not be accepted.
•	Samples are limited to the P1 level defined in "the Law concerning the Conservation and Sustainable Use of Biological Diversity through Regulations on the Use of Living Modified Organisms" (Cartagena Protocol) issued by Ministry of Education, Culture, Sports, Science and Technology.
•	The data of the regions just after sequence primers has lower reliablity. Please consider this in advance.
•	Data are gained by the Double Strand sequence analysis using Forward and Reverse primers for higher reliability. The recommended size of PCR product is between 300bp to 500bp.
•	Please provide the reference sequence and known SNP information by electronic file.
•	In case of the additional analysis for the ROI sequence that had been ordered before, order from one sample will be accepted. Please state the previous order number on the order sheet.
•	If the additional analysis is required, please contact within three months after the analysis (our data retention term). Thank you for your understanding.
•	Sample is subject to quality control upon receipt by agarose gel electrophoresis. The order might not be accepted if the result of quality control suggests the difficulty of analysis. Thank you for your understanding.

How to send the reference sequence and known mutation information

Reference sequence is the sequence to be used for comparison.
Please provide the target gene information such as gene name, accession No., region of interest (ROI). Please write any known mutation information you have in the special sheet for it.

*	Sequence analysis is basically by Double Strand analysis using FW and RV Primers.
*	In this service, one SNP analysis includes the sequence comparison that can be analyzed within the reach of one sequence reaction (ca. 500bp).
*	Please ask separately if the comparing region is more than 500bp.
*	Waveform data reliability will be lower in the region just after the primer. It is recommended to set ROI more than 100bp inward from the sequence primers.

<How to send known mutation information>
Please enter the known mutation information in "known mutation information sheet" that attaches to order sheet as instructed below.

How to fill in the sheet

Type:	Select one from the next three types: Base Change / insertion / deletion
ROI:	Write down the name of ROI with mutation. (in case ROI are more than one.)
NT position: Reference: Variant:	Example)
	1) Base Change : 356-TGGCACGC-363 356-TGGAACGC-365 NTposition = 359 / Reference = C / Variant = A
	2) Insertion : 356-TGGC\|ACGC-363 356-TGGCTACGC-364 NTposition = 359 / Reference = C / Variant = T
	3) Deletion : 356-TGGCACGC-363 356-TGG***GC-360 NTposition = 359 / Reference = C / Variant = vacant
Description:	The contents in this sheet will be shown in the mutation list as additional information at the detection of mutation location. In order to avoid problems against the software used, please use one-byte alphabetical / numeric characters without space.

Example of known mutation information filling

Known mutation information sheet