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Longer read length, wider application - MGISEQ-2000RS high-throughput sequencing reagent kit now available (SE400)

2019-06-26

MGISEQ-2000RS High-throughput Sequencing Reagent Kit (SE400) is a new addition to the MGISEQ-2000RS product line of the flagship high-throughput gene sequencer. It is more suitable for long fragment amplicon sequencing, which requires longer single-ended sequencing reads. Field applications, such as short tandem repeats (STR) are widely used in forensic identification with a fragment length of 100-500 bp. The short tandem repeats in the middle result in the inability to use pair-end sequencing to splice two reads into one. The MGISEQ-2000RS high-throughput sequencing reagent kit (SE400) is now commercially available, and the performance is outstanding. The single-ended sequencing read length is 400bp, and the data quality is excellent, which further expands the applications of high-throughput sequencing technology in forensic identification.


I. Product performance of MGISEQ-2000RS high-throughput sequencing reagent kit (SE400)

MGISEQ-2000RS high-throughput sequencing reagent kit (SE400) performance parameters

Sequencing read length

SE400+10

Run time*

109 hours

Total Reads /Slide**

1500~1800M

Q30***

70%

* Run time, include DNB loading, sequencing, and data processing time.

** Total Reads /Slide is based on a specific standard library, the actual application performance will be fluctuant according to the sample types and quality of library, insert size and other factors.

*** Q30 is based on a specific standard library, the actual application performance will be fluctuant according to the sample types and quality of library, insert size and other factors.

II. Basic Data

To validate the performance of the MGISEQ-2000RS High-throughput Sequencing Reagent Kit (SE400), we ran 10 slides and 40 lanes on 5 MGISEQ-2000RS sequencers, including 15 E. coli (450 bp) libraries, and some application sample libraries such as WGS, STR, etc.


Figure 1 E. coli (450bp) sample SE400 data performance

Total reads/lane 460M, CV=1.82%

Q30 76%, CV=1.24%

Split rate 95%, CV=1.41%

The data showed that the MGISEQ-2000RS high-throughput sequencing reagent kit (SE400) was stable on the E. coli (450 bp) library in terms of total reads, Q30 and Split rate.

The quality values were excellent. Using the same library, testing PE300 on the I platform, and testing the SE400 on the MGISEQ-2000RS, comparing the 300 bp of Read1 of the I platform PE300 and the 400 bp of the MGISEQ-2000RS platform, the values are as follows:

Figure 2: Quality values of 400 cycles of the MGISEQ-2000RS High-throughput Sequencing Reagent Kit (SE400)


Figure 3: Quality values of 300 cycles of Read1 on the I platform PE300


III. Application result


STR_SNP forensic project:

Short Tandem Repeats (STR), also known as microsatellite DNA, are a class of DNA tandem repeats that are widely found in the human genome. The STR sequence has 2-6 bases as the repeat unit, repeats 5-40 times, the total repeated fragment length is 100-500 bases, and more than 8000 STR loci have been found in the human genome. Due to the high polymorphism between individuals in STR loci, STR is widely used in individual identification, criminal case detection, paternity testing, etc. Currently, capillary electrophoresis (CE) is widely used in STR detection. By fluorescent color and STR length typing, CE-STR technology can detect 6-8 fluorescent colors, and can amplify about 34 STR loci. It has played a key role in STR application for more than 20 years. However, in the context of the large increase in sample size and in difficult cases in recent years, the detection flux and the inability to obtain sequence information create limitations. The application of high-throughput sequencing for STR typing can effectively solve the problem of detection flux, and at the same time, the polymorphism of STR locus sequence can be obtained, which is especially important when the number of acquired sites is limited. Compared with capillary electrophoresis, high-throughput sequencing can detect more than 120 STR loci in a single reaction, combined with third-generation genetic markers, single nucleotide polymorphisms (SNPs). Individual identification SNPs, appearance features SNPs, ABO blood group SNPs, ancestral SNPs, mitochondrial DNA polymorphisms, etc. can be obtained in a single reaction, showing a strong expansion and a broader application prospect.


For STRs, due to the 100-500 bp short tandem repeats in the middle, it is not possible to splice two reads into one using pair-end sequencing. The MGISEQ-2000RS high-throughput sequencing reagent kit (SE400) has a single-end read length of 400 bp. The quality and yield are stable, which increases the accuracy of STR classification and expands the further application of high-throughput sequencing technology in forensic identification. Based on the MGISEQ-2000RS High-throughput Sequencing Reagent Kit (SE400), it performs well in forensic projects:


Test Methods

Simultaneous 63 STR + 166 SNP sites were detected by single tube method, using SE400+10 sequencing strategy


Str classification consistency (taking 20 FBI CODIS sites as an example):

Sample: NA12878

The consistency of STR length polymorphism detected by CE-STR technology and high-throughput sequencing amplicon technology is 100%;

The consistency of the MGISEQ-2000RS platform and I platform detection based on the flux sequencing amplicon technology was 100%.

Locus

CE

I

MGI

Typing consistency

D1S1656

14,15.3

14,15.3

14,15.3

Consistent in length and sequence

TPOX

8

8

8

Consistent in length and sequence

D2S441

11,14

11,14

11,14

Consistent in length and sequence

D2S1338

17,20

17,20

17,20

Consistent in length and sequence

D3S1358

16,17

16,17

16,17

Consistent in length and sequence

FGA

22,24

22,24

22,24

Consistent in length and sequence

D5S818

12

12

12

Consistent in length and sequence

CSF1PO

10,11

10,11

10,11

Consistent in length and sequence

D7S820

8,10

8,10

8,10

Consistent in length and sequence

D8S1179

12

12

12

Consistent in length and sequence

D10S1248

15,16

15,16

15,16

Consistent in length and sequence

TH01

7,9.3

7,9.3

7,9.3

Consistent in length and sequence

vWA

15,17

15,17

15,17

Consistent in length and sequence

D12S391

16,17

16,17

16,17

Consistent in length and sequence

D13S317

11,12

11,12

11,12

Consistent in length and sequence

D16S539

10,11

10,11

10,11

Consistent in length and sequence

D18S51

16,17

16,17

16,17

Consistent in length and sequence

D19S433

12,14

12,14

12,14

Consistent in length and sequence

D21S11

30

30

30

Consistent in length and sequence

D22S1045

13,15

13,15

13,15

Consistent in length and sequence


SNP typing consistency:

Sample: NA12878

A total of 166 sites were detected

There were 82 identical SNP in the kit with I platform, and the typing rate of the detection site was 100%.

Locus

I

MGI

Consistency

rs1005533

GA

GA

Consistent

rs10092491

TC

TC

Consistent

rs1015250

GG

GG

Consistent

rs1028528

AA

AA

Consistent

rs10495407

GA

GA

Consistent

rs1058083

GG

GG

Consistent

rs10773760

AG

AG

Consistent

rs1109037

GG

GG

Consistent

rs12997453

AG

AG

Consistent

rs13218440

GG

GG

Consistent

rs1360288

CC

CC

Consistent

rs1490413

GA

GA

Consistent

rs1493232

AA

AA

Consistent

rs1498553

CT

CT

Consistent

rs1523537

CC

CC

Consistent

rs1528460

CT

CT

Consistent

rs159606

AG

AG

Consistent

rs2040411

AA

AA

Consistent

rs2056277

CC

CC

Consistent


With rapid advances in technology, we believe the MGISEQ-2000RS high-throughput sequencing reagent kit (SE400) will bring distinct benefits to your research.

MGISEQ-2000RS High-throughput Sequencing Set (SE400) is available now!

Product Name

Version No.

Item No.

MGISEQ-2000RS High-throughput Sequencing Set (SE400)

V3.1

1000013857


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