7
REVEAL GREATER COVERAGE DEPTHI N WHOLEEXOME SEQUENCI NG Achieve greater coverage depthfrom less sequencing through theenhanced coverage of the new SeqCap EZ MedExome T arget Enrichment Kit for wholeexome sequencing. Rely on a design developed to enrich the entireexome (Figure 1),but particularly optimized for analyzing regions of medical relevance (Figure 2) in research studies. ï Focus on genomic regionsthatreally matter For disease-associated genes, 98% of bases are covered at ˇ20X depth. ï Call variants with conˇdence Detect SNPs with98%sensitivity and >99% speciˇcity for SNP allele classiˇcation. ï Gain greater efˇciency at minimal cost Reduce sequencing cost through uniform coverage (Figures1 and 3) and fully supported multiplexing protocols.

REVEAL GREATER COVERAGE DEPTHIN WHOLEEXOME SEQUEN€¦ · Roche MedExome Supplier Aí Clinical Research Exome Fold80 Base Penalty Fold additional sequencing needed to bring 80% of

  • Upload
    others

  • View
    0

  • Download
    0

Embed Size (px)

Citation preview

Page 1: REVEAL GREATER COVERAGE DEPTHIN WHOLEEXOME SEQUEN€¦ · Roche MedExome Supplier Aí Clinical Research Exome Fold80 Base Penalty Fold additional sequencing needed to bring 80% of

REVEAL GREATER COVERAGE DEPTH IN

WHOLE EXOME SEQUENCING

Achieve greater coverage depth from less sequencing

through the enhanced coverage of the new SeqCap EZ

MedExome Target Enrichment Kit for whole exome

sequencing. Rely on a design developed to enrich the

entire exome (Figure 1), but particularly optimized

for analyzing regions of medical relevance (Figure 2)

in research studies.

ï Focus on genomic regions that really matter

For disease-associated genes, 98% of bases are

covered at ˇ20X depth.

ï Call variants with conˇdence

Detect SNPs with 98% sensitivity and >99%

speciˇcity for SNP allele classiˇcation.

ï Gain greater efˇciency at minimal cost

Reduce sequencing cost through uniform

coverage (Figures 1 and 3) and fully supported

multiplexing protocols.

Page 2: REVEAL GREATER COVERAGE DEPTHIN WHOLEEXOME SEQUEN€¦ · Roche MedExome Supplier Aí Clinical Research Exome Fold80 Base Penalty Fold additional sequencing needed to bring 80% of

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150

Percentofbases

Depth of coverage

Roche MedExome Supplier Aís Clinical Research Exome

Fold 80 Base Penalty

Fold additional sequencing needed to

bring 80% of the targeted bases up to

the original mean coverage depth

MedExome 1.95

Competitor A 2.21

0.0

10.0

20.0

30.0

40.0

50.0

60.0

<90% 90-97% 97-100% 100%

PercentoftotalGeneTestsgenescovered

Percent of each GeneTests geneís coding bases covered at ˇ20X

Roche MedExome Supplier A's Clinical Research Exome

Figure 1. Rocheís SeqCap EZ MedExome kit demonstrated

sustained coverage at 100% and more uniform coverage than

Supplier Aís Clinical Research Exome. Fold 80 base penalty

calculation shows more uniform capture for the SeqCap EZ MedExome

Kit. This graph is of one representative sample from one 6-plex capture

per product. For Supplier Aís product, the targets are unpadded.

SeqCap EZ MedExome kit target reˇects empirical target across all

metrics. All reads were subsampled to 60 million for assessment.*

Figure 2. With SeqCap EZ MedExome, 53% of medically relevant

genes are covered at 100% (ˇ20X coverage) vs. 6% by Supplier Aís

Clinical Research Exome. Percentage of bases covered at ˇ20X for each

consolidated target was determined using GATK (DepthOfCoverage),

summarized by gene. Supplier A kitís data was generated by a third-

party sequencing service provider, following Supplier Aís protocol. All

reads were subsampled to 60 million for assessment, then subjected to

the same bioinformatics pipeline for analysis.*

For patent license limitations for individual products please refer to:

www.technical-support.roche.com

NIMBLEGEN and SEQCAP are trademarks of Roche.

All other product names and trademarks are the property of their respective owners.

© 2016 Roche PP-US-05710-0816

Roche Diagnostics Corporation

9115 Hague Road

Indianapolis, Indiana 46256

For life science research only.

Not for use in diagnostic procedures.

Reveal more about the exome

Learn more about how the SeqCap EZ

MedExome Target Enrichment Kit can

improve your whole exome sequencing. Visit

sequencing.roche.com/medexome.html

or call 800-262-4911.

* Roche data on ˇle.

Supplier Aís Clinical Research ExomeRoche SeqCap EZ MedExome

Figure 3. SeqCap EZ MedExome shows reduced GC bias in

sequencing coverage with uniform coverage over a broad range

of GC content. One-hundred nanograms of extracted NA12898 DNA

was subjected to performance evaluation by both kits. Performance was

determined post-enrichment following SeqCap EZ Userís Guide v5.1.

Supplier Aís kit data was generated by a 3rd party service provider

following vendorís protocol. All reads were subsampled to 60 million for

assessment. Sequencing reads were subjected to the same bioinformatics

pipeline for analysis. GC composition of all consolidated target regions

(empirical target for MedExome, unpadded target for Supplier A) was

determined and plotted against mean depth of coverage calculated by

GATK DepthOfCoverage for all consolidated target regions.*

Page 3: REVEAL GREATER COVERAGE DEPTHIN WHOLEEXOME SEQUEN€¦ · Roche MedExome Supplier Aí Clinical Research Exome Fold80 Base Penalty Fold additional sequencing needed to bring 80% of

AAASmembers harness the power of scientifc

thinking to help tackle complex, global challenges.

Join the community of scientists, engineers,

and educators whose work impacts millions.

How will YOUmake your mark in science?

Join AAAS today.

www.aaas.org/join

A M E R I C A N A S S O C I A T I O N F O R T H E A D V A N C E M E N T O F S C I E N C E

BETHE CORE

OFSCIENCE.

MIND SPIRIT FACE

HEARTVOICE

REACH

CENTER

Page 4: REVEAL GREATER COVERAGE DEPTHIN WHOLEEXOME SEQUEN€¦ · Roche MedExome Supplier Aí Clinical Research Exome Fold80 Base Penalty Fold additional sequencing needed to bring 80% of

Image:jim

/AdobeStock

NOW ACCEPTING

MANUSCRIPTS

ScienceRobotics is a unique journal created to help advance the research

and development of robotics for all environments. Science Robotics will

provide a much-needed central forum to share the latest technological

discoveries and to discuss the feld’s critical issues.

Join in the excitement for the Fall 2016 debut!

ScienceRobotics.org

Be Among the First to Publish

in Science Robotics

Page 5: REVEAL GREATER COVERAGE DEPTHIN WHOLEEXOME SEQUEN€¦ · Roche MedExome Supplier Aí Clinical Research Exome Fold80 Base Penalty Fold additional sequencing needed to bring 80% of

26 AUGUST 2016 • VOL 353 ISSUE 6302 937 SCIENCE sciencemag.org/custom-publishing

LIFE SCIENCE TECHNOLOGIESNEW PRODUCTS

Produced by the Science/AAAS Custom Publishing Office

Electronically submit your new product description or product literature information! Go to www.sciencemag.org/about/new-products-section for more information.

Newly offered instrumentation, apparatus, and laboratory materials of interest to researchers in all disciplines in academic, industrial, and governmental organizations

are featured in this space. Emphasis is given to purpose, chief characteristics, and availability of products and materials. Endorsement by Science or AAAS of any

products or materials mentioned is not implied. Additional information may be obtained from the manufacturer or supplier.

pH Electrodes

YSI showcases a strong set of pH

measuring options for the lab. The Io-

Line electrodes host a unique iodine/

iodide reference system with a patented

three-chamber reservoir system. IoLine

$%$&'���$����$�����$'�%$��'�%'��� �'�

�$�����$�'�$����������&&��&��'�

a higher speed compared to traditional

silver/silver chloride (Ag/AgCI) reference

systems. They have a 100% metal-ion-

�$$��$ $�$�&$����'$�������$��$%� ���

�������$����%�'������&���%$����'$&��

applications such as immunoassays. YSI

�����$������$%$&'�$��%$&'���$����$�����

�$�%%�%$�$%$&'���$�� ��������$�$�'����-

eters. Each electrode comes supplied with

�$ $�$�&$��%%���%�'��������&��'�$��'���-

���'����������''%$�� �&%��'����'������

so the electrode can be used right away.

�&�$������'��$$ �$��!���'���������

and MultiLab meters are easy to use and

&��$������%$����%�����'��%$�&���$%�"�

The MultiLab meters are available with In-

'$%%�$�'�#�'%��$�����'$&���%������'$��%�

�$�������������'��%���%' �����'$�"�

Xylem

For info: 978-778-1010

������/.��0��

�������������� �

��.� 0!�.������"� #���/�.���������

�0����0���1�/.��0���.�1�1����/1�.�

0���.�1�����/�.���.�./��.����.0�0//��

for use with vacuum ultraviolet (VUV) sili-

con photodiodes. With its integral sock-

.1.�����1����.�����1��1�.�0����1���

�.1.01��$��/�.��������0���.���.��1��

measure small photogenerated currents

with resolutions of 10 femptoampheres

and dynamic ranges of four orders of

���1��.����.��"� #�0����1��� ���.���

/������.���.�1�����/�.���1����.-

lectable feedback resistor. The feedback

resistor is also socketed and may be

changed to match the gain and dynamic

���.��.%��.�.�1��� ����.��.��.�1��

McPherson VUV series photodiodes are

��.�� ���1�.��.1.01���� �&���.�1�.�.�&���

���#����'��./.��1�����.����((����1��

��)*�����.�.�������.����+�.��1�����.�,�

���1������//�0�����.�1���.�/���1�/.��0.���.��/1�����0����1.�1�

0���.�1�1����/1�.�1��� .��0��01.��10���1�����/����.1���/1-

�.���1�����/���1���1�1�.����1����.����-��������.������/��

required for operation.

McPherson

"������#�$�%����� ���

www.mcphersoninc.com

Comet Assay Microplate

��'��'��$���'((�&��'*&� ���*'��

enables reproducible and sensitive

measurements of DNA damage in

human cells and provides the necessary

*������ �*������'��*��)*�*'�*���������

�'�'(� �'�*��' �'��(��)�(��*��'���

and clinical assays. Instead of being

randomly dispersed in agarose on a glass

�(�'������*�'�*���*���(�&��'*�������

cells in the CometChip are captured on

an array of agarose microwells. Each well

���*�'�&��'*&� �)��*����� �����*'(�

����)���'((�����!���)�������'*'���

�� (�'�������'��'�� �**'��������' *��

that causes the captured test cells to

�'��'��������('� (��'�������('�$���'((�

&��'*&� �)��� ����)'����������*��

��*�� '��)� �����'����������'���'�

of 208 cells imaged per well. With a

)� �)*�����*��''�&��'*&� �� '�������

the output for just two runs per day is

����������*�� ��*�����'�&��'*����(���

Software can analyze data from these

�����00 cells and generate a report in

under 20 minutes.

AMS Biotechnology

��������������������� � ���

www.amsbio.com

PTR-MS Autosampler

The real-time measuring capability

of a proton transfer reaction-mass

spectrometry (PTR-MS) trace gas

analyzer is ideally suited for continuous

volatile organic compound (VOC)

���%��������%��#��������� �����#���

of discrete samples within seconds.

The new IONICON autosampler for

PTR-MS enables automated screening

of hundreds of sample vials. It can

be loaded with multiple sample trays

carrying up to 270 vials (20 mL)

���#%��"���#������#�������#����������

samples. The benchtop autosampler

allows for static and dynamic headspace

measurements. A custom-made software

controls the sampling process as

well as the PTR-MS measurement for

integrated and consistent data. Several

preprogrammed sample treatment

�������#��� ��%�$�#��$����"����%�"��� %�!"������� "$�$�

� #$�%�����������##��%"���%"�������%������ �%���%"������

VOC headspace analysis drastically reduces processing costs

for larger batches of samples and provides high-quality data.

Ionicon

*������+�/'(�$%)���&�&�'�,%%

www.ionicon.com

Milling Platform

The Fitzpatrick Company and Quadro

Engineering Corp. have launched

8�5��7�6��65�������85��$���)��8�5�

latest incarnation of their lab-scale

����*8. 66�����#��-��6�7�����-

tion package. The SLS includes

��5���85��6� ��75����������66���

solutions: Fitzpatrickís FitzMill L1A

-�����8��������0�����1��#������

#��2����375�7�-��6��*65���8�

��������2��2�����5����!��-��6��

Operators can alternate between

��68 65��66�����6�8���������85���

due to its innovative tri-clamp design.

The equipmentís head interchange-

ability makes it suitable for milling

���"����58���85��6�7���8������

������8�����6��5�����8��7�� 65�5�8�

lab-scale wet granulation systems.

It enables operators to process

��� 65��������66���������8������6�

6������� ����78��585�8��������7���

�7�5�5�4�%���"����66�������75�8���

products. The SLS utilizes ìsmart-

detectîóa feature that automatically

ensures the appropriate speed range

����5�����57���.���8�5��5����5���

installedóto ensure that scalability to

production machines is maintained.

The Fitzpatrick Company

*������+��(%��(%�((((

�����8.�66�7��

Page 6: REVEAL GREATER COVERAGE DEPTHIN WHOLEEXOME SEQUEN€¦ · Roche MedExome Supplier Aí Clinical Research Exome Fold80 Base Penalty Fold additional sequencing needed to bring 80% of

@SciMagWebinars

antibodies

apoptosis

biomarkers

cancer

cytometry

data

diseases

DNA

epigenetics

genomics

immunotherapies

medicine

microbiomics

microfuidics

microscopy

neuroscience

proteomics

sequencing

toxicology

transcriptomics

VIEW NOW!

webinar.sciencemag.org

Learn about the latest breakthroughs, new

technologies, and ground-breaking research

in a variety of felds. Our expert speakers

explain their quality research to you and

answer questions submitted by live viewers.

watchourwebinars

technologies?want new

Brought to you by the Science/AAASCustom Publishing Ofce

Page 7: REVEAL GREATER COVERAGE DEPTHIN WHOLEEXOME SEQUEN€¦ · Roche MedExome Supplier Aí Clinical Research Exome Fold80 Base Penalty Fold additional sequencing needed to bring 80% of

Are yourexosomes tellingyou everythingthey know?

Extracellular vesicles like exosomes can provide useful insights into

cellular physiology and are a great source of circulating biomarkers.

But are you getting all the information you can from them?

Let the experts at System Biosciences (SBI) help with our

start-to-finish exosome profiling services:

Exo-NGS • Proteomics • Nanosight • Lipidomics

Just send us your samples, we’ll take care of the rest.

Now offering new low pricing! Find out just how low—email us at

[email protected]