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NewsTrack Summer Issue 2012Volume 2 Issue 3

BlueGnome update

Celebrations at BlueGnomeThis quarter has been a busy one for celebrations, not only have we celebrated our 10th Anniversary but we were also the recipient of a Queen’s Award for International Trade.

BlueGnome was founded in 2002 by a team of scientists who developed a novelmathematical technology for the analysis ofgenetic data. In 2006, the first CytoChip was launched followed by 24sure in 2008. BlueGnome hasbeen consistently growing over the past 10 years and thisyear we moved to new premises and have been expanding in all areas of the business.

We were very pleased to be awarded the Queen’s Award for International Trade for the first time. This was awarded for a sustained increase in export earnings over three 12-monthperiods. Our expansion into over 40 countries includes setting up operations in key markets in North America, and Asia inaddition to existing markets in Europe. As we grow, receive awards and celebrate our 10 years in business our philosophy still remains the same and we endeavour to maintain our core values.

We thank you for supporting our business during the past 10 years and hope that you continue to do so.

www.cytochip.comwww.24suretest.com

Welcome to the Summer issue ofNewsTrack. Since joining BlueGnome in March I’ve been busy with variousmarketing activities, however this is myfirst NewsTrack and it’s really exciting topull together all of the news items overthe past 3 months and consolidate themfor you - it’s actually quite amazing to lookback at everything that’s happened. Jessis still here and will continue to contributeto NewsTrack however Jess is nowworking on other projects, which she’lltalk about in her sections.

This quarter we've held 3 user groupmeetings in Europe, launched BlueFuseMulti v3.0 and CytoChip Focus 8x60kand introduced a number of new faces to the BlueGnome team. We've updatedboth our 24sure brochure and publicationbooklet and have put together a newbrochure and publication booklet forCytoChip Focus. We continue with ourschool outreach programme and havebeen welcoming visitors to Cambridge fortraining. BlueGnome has been in thenews quite a lot this quarter, particularly

for 24sure and we were awarded aQueen’s Award for Enterprise inInternational Trade.

Jess has been busy making videos forboth training and support and we'vestarted putting together some morepromotional videos for our products. This issue we feature an interview withNicole Bain who has been a BlueGnomepostnatal customer for some years and is now running a pilot study to investigatehow to best implement array testing in the prenatal setting.

I hope that you enjoy this issue ofNewsTrack and we will endeavour to keep you informed of news “as ithappens” through emails to ourcustomers and regular tweets. If you feel that you’re not receiving these emails, please let me know and of course follow BlueGnomeLtd on twitter.

Sally [email protected]

In this issue

BlueGnome update

Celebrations at BlueGnome

New faces

New literature

Focus on the sales team

News from India

School visits

New products

Review of user group meetings

Document versioning

BlueGnome in the news

Interview with Nicole Bain

Julie's news

Movies

NewsTrack FINAL_Layout 1 18/07/2012 10:05

This quarter a number of new faces have joined the team at BlueGnome both in theUK, North American and Asian offices. The new roles cover sales, support, finance,software and the lab. A number of new chairs arrived at our Cambridge office recentlyand looking at the careers section of our website, I’m sure we’ll announce even morenext quarter!

New faces

Theo KingshottDistribution ManagerTheo joins us as Distribution Manager. Hehas 15 years experience of internationalchannel partner management. There arehuge opportunities for BlueGnome inemerging markets and Theo will befocusing on setting up partnerships thatcan deliver long term growth and upholdBlueGnome’s values locally.

Siow Leng SimMicroarray Application Specialist Siow Leng joins us as a MicroarrayApplication Specialist at our Singaporeoffice, working closely with Tai Wai.Previously he was with A-Bio Pharma astheir Project Manager for pre-clinicalbiologics R&D and production projects.Siow Leng obtained his PhD in Chemicaland Biomolecular Engineering from theNational University of Singapore.

Dan SaulNorth American Microarray Application SpecialistDan joins us from the Johns HopkinsHospital where he was the technical leadof the CLIA and CAP accredited PrenatalCytogenetics Laboratory. Prior to this role,he was the supervisor of MolecularCytogenetics at GeneDx. Dan will serve as a new USA support representativebased on the East Coast.

Simon ShawTest/Software Engineer

Andy JoadLab Technician

Updated versions are now available of the 24sure brochure and 24surepublication booklet, plus we now have a CytoChip Focus brochure andCytoChip Focus publication booklet. All literature is available to download as pdfs from our website, and hardcopies can be requested [email protected]

New literature

Setting new standards in IVF

Clear results fromchallenging cases

Kathryn GreyFinance Assistant

Suknya Rani-ThomsonLab Technician


In June BlueGnome welcomed a teamfrom Sir Ganga Ram Hospital in NewDelhi to Cambridge for training. TheCenter of Medical Genetics at SirGanga Ram Hospital was established in 1997, and is the leading centre forGenetic services in India. Patients arereferred for genetic counselling andtesting from all over India, as well asfrom Bangladesh, Pakistan, Nepal,Afghanistan, Sri Lanka, and UAE. TheCytoChip will be the first array platform to be used clinically at Sir Ganga Ramhowever with over a billion people inIndia, and a population projected tosurpass China in 2025, we areoptimistic that the first shipment of arrays will not be the last.

News from India

The BlueGnome sales team continuesto grow in response to the strongdemand for our products and servicesacross the globe, with new hires insales in the last quarter. We are now

Focus on the sales team

In April we welcomed two six form groups to BlueGnome as part of ourschools outreach programme. During the course of the two days, students wereintroduced to the practical application ofmathematics and biology in a fullyintegrated biotech like BlueGnome. Inaddition to a tour of our new R&D andproduction facility the students receivedpresentations from different BlueGnome

School visitsscientists on the roles that they perform in the company. The decision of onestudent to investigate a degree inbioinformatics rather than historyillustrates the limited information onwhich potential scientists make theseimportant career decisions and thepotential of companies like BlueGnometo make a practical difference to this process.

represented in North America, APAC and Europe with direct sales managers, an office-based Inside SalesRepresentative and a new position of Distribution Manager.

The newly expanded team met together recently in Cambridge to share experiences and learn about our new products.

www.cytochip.comwww.24suretest.com


New products

BlueFuse Multi v3.0We are pleased to announce that BlueFuse Multi v3.0 is nowavailable to download from our website www.cytochip.comusing your normal web logins. The major feature of this releaseof BlueFuse Multi is to support simultaneous write access tothe database by multiple users. In previous versions only asingle user could write to the database at one time and thiscould create workflow bottlenecks for customers with largenumbers of users. If you require the Multi user write facilityoffered by BlueFuse Multi v3.0 it is necessary to install twodifferent programs: BlueFuse Fuse Multi v3.0, onto eachworkstation where it’s needed and BlueFuse Server v3.0 ontothe server location. Other than that there are few changes tothe BlueFuse Multi setup; if you wish to use ‘Server’ mode tickthe check box as shown below, if not checked, BlueFuse Multican continue to be used in ‘Classic’ mode (akin to the previousversions of BlueFuse Multi).

We have alsoincorporated aregion details boxthat allows usersto annotateregions with theirown comments(present onGenome Viewshortcut). Thesecomments are

tracked within the database by the user who made them andthe time. Comments also appear on the report, so it is noweasy to see why a particular decision was made.

Importantfeatures for24sure V3 usersincluded in thisrelease are:improvementsto the analysisworkflow of24sure V3experiments andan update to thereference strategy. Previously it was necessary to create two batch import files for each batch of experimentsperformed, one for the reference hybridizations and a secondto import the samples. In BlueFuse Multi v3.0, a single batchimport file, that contains details of both reference and samplehybridizations, is supported and reference databases arecreated fully automatically.

A second important part of BlueFuse Multi v3.0 release for24sure V3 customers is an update to the protocol whichinvolves a small change to the reference strategy. Following abeta trial we have determined that we achieve better resultswith a sex matched reference strategy as opposed to theprevious sex mismatched set up. With the new protocol it is

simply a case of running one of the reference hybridizationareas as male vs male, and the second as female vs female,results in much better gender chromosome calling, reducingboth the noise on the sex chromosomes and more significantlythe potentially misleading shift towards gain and losses on Xand Y that can result in ambiguous calling of these samples. A document outlining this change can be seen www.cytochip.com/protocol_docs titled 24sureV3 updated referencestrategy.pdf.

To facilitate both the single batch import and the sex matchedreference strategy for 24sure V3 users, a new 24sure V3planner spreadsheet has been produced, fully populating thebatch import file for use directly into BlueFuse Multi. The new laboratory planner is available fromwww.cytochip.com/protocol_docs and is called 24sure V3 planner V2 - 7 June 2012.

Other new features in the latest release of BlueFuse Multi include: • Algorithm settings can now be applied on a per-

experiment basis.• The set of columns to display in

the CGH table is now configurable.• Import of Custom BED files has been improved.• Drop down lists of arrays now include the array design ID

next to the array name.

For release notes and full details of how to install and upgradeBlueFuse Multi, please see the Installation Guide also availableon our website. If you have any further questions on anymatters relating to BlueFuse Multi please contact us [email protected]

CytoChip Focus 8x60KRecent large scale studies (1000+ samples) have shown a benefit of using microarray-based approaches to detectrelevant copy number imbalances when analysingchallenging samples such as amniocentesis and chorionicvillus sampling (CVS). The second product release for thisquarter is a new microarray design: CytoChip Focus 8x60K.This microarray mimics the design of CytoChip FocusConstitutional BAC platform, but applied to an oligoplatform, improving the cost effectiveness of the approachin high throughput applications, the resolution of detectionand also slotting into the workflow of laboratories who areequipped to run oligo arrays routinely. The design includesprobes on 162 constitutional genes selected from the ISCAlist, with a focus on severe early developmental disorderswith coverage of genes associated with late onset disorders having been removed. In addition the design hasbeen optimised to avoid the confusion of reporting onvariants of unknown significance (VOUS). For furtherinformation on CytoChip Focus please visit our websitewww.cytochip.com/productfocus and check out our new brochure and CytoChip Focus publication booklet.


This quarter we’ve hosted 3 user group meetings all of which were very well attended. User group meetings allow our customer communities to get together and learn more aboutour products from us, but perhaps more importantly from eachother; learning best practices, how others use our products, andexchange of ideas. First was our European User Group Meetingin Darmstadt, Germany, which covered all BlueGnome products.We were very pleased with the turnout, especially those peoplewho had travelled from other countries or from the other end ofGermany to attend the meeting.

Second was our first 24sure specific user group meeting,which was held in Bregenz, Austria during the PGDIS meeting. In the morning we held an arrayCGH workshop inconjunction with the congress, and then in the afternoon heldour user group meeting. There were over 60 people attendingboth events, which was a great turnout.

The third of our user group meetings was held here inCambridge, at BlueGnome's headquarters and was attendedby both our cytochip and our 24sure users from the UK. Userslistened to a range of talks and during their lunch break hadtours of our new facility.

For all meetings, we were lucky enough to secure veryinteresting speakers, ranging from those talking about projects

Review of user group meetings

Document versioningPlease see the table below for updates to protocols since they were last published. The recent updates have been mainly due to the inclusion of the BlueGnome’s ClearScan microarray scanner into the 24sure V3, 24sure and CytoChip protocols and alsothe change in reference strategy for 24sure V3 protocols to a sex matched design. The current versions of the summary protocols and reference manuals are on www.cytochip.com and summary protocols areincluded with all deliveries.

24sure V3 laboratory protocols

1.5 8th May 2012 Inclusion of ClearScan microarray scanner

1.6 29th May 2012 Change reference strategy to sex-matched design

1.7 11th June 2012 Amended reference in step A5.2

CytoChip protocols

3.9 16th April 2012 Inclusion of ClearScan and ClearScan Auto to the Equipment list.

CytoChip Oligo protocols

No changes

24sure dual channel protocols

1.8 16th April 2012 Inclusion of ClearHyb Hybridization and ClearHyb Wash System in the main protocol.Preparation of amplification controls moved to main protocol. Update of model numbersand company address.

1.9 11th June 2012 Inclusion of ClearScan microarray Scanner. Amend reference in step A5.2

that they were starting to those reporting results. Some of themtalked about unusual results, some talked about challengesthey’ve been having, and others introduced new technology.

We are always interested in hearing about the work that ourusers do. If you are interested in giving a talk at a user groupmeeting we would love to hear from you.

Please contact [email protected]

Our North American and Asian User Group Meetings, areplanned for later in the year. Look out for details of those!


BlueGnome in the news

The field of IVF is often in the news and this quarter has been no exception. The highlight for us was the publication of the Yang et al paper (MolecularCytogenetics 2012, 5:24) “Selection ofsingle blastocysts for fresh transfer viastandard morphology assessment aloneand with array CGH for good prognosisIVF patients: results from a randomizedpilot study”.

This paper announced the results of thefirst randomised prospective IVF study of preimplantation chromosome analysisusing 24sure. Yang et al., demonstratedthat selectively implanting euploidembryos (single embryo transfer), with a normal number of chromosomessignificantly increases pregnancy rates.The results provide direct evidence that24sure analysis can deliver a 65%increase in pregnancy rates, even inyounger patients with more favourableIVF outcomes.

Pacific Health Reproductive are nowbeginning to report the births of healthybabies from the study (see photo).

This landmark study using 24sure waspicked up by a number of media outlets,most notably, the story featured as tophealth story on the BBC Health Newshttp://www.bbc.co.uk/news/health-17942176 and the scientific paper hasbeen downloaded nearly 4,000 times.

We also announced clinical trials with 2 of the world’s leading IVF centres: IVI in Spain, and Reprogenetics in the US.

Both studies will be investigating thebenefits of 24 chromosome aneuploidyscreening using 24sure.

Specifically, IVI will be comparingrandomised results from 120 cycles ofthe most challenging IVF patients; womenfrom 38 to 40 years and men with severeoligozoospermia, in which 24sure PGS isused to select embryos for implantationagainst 120 cycles in which PGS is not applied.

Reprogenetics will compare a controlgroup who will have up to 2 embryosimplanted on day 5 based ondevelopmental characteristics, with a testgroup who will have blastocysts biopsiedon day 5, PGS performed with 24sure,and a single euploid embryo transferredon day 6. Recruited patients (110 in eacharm) will be randomised on day 5.

We await the results with anticipation.

The most recent news item we havepublished reports a great achievement byREPROMEDA who have achieved ISO15189 accreditation for use ofBlueGnome’s 24sure platform for theirlaboratories in Brno, Czech Republic.This accreditation provides patients withthe reassurance that their method oftreatment and preimplantation diagnosisis officially accredited and provides abasis for other laboratories to follow.

ISO 15189:2007 is for use by medicallaboratories in developing their qualitymanagement systems and assessing

their own competence, and for use byaccreditation bodies in confirming orrecognising the competence of medicallaboratories. This accreditation isapplicable for all medical laboratories.

If you have news items relevant to our products that you would beinterested in sharing with us, we would be happy to help publicisethem. Contact [email protected]

Dr. Yang holding the first baby born from his study published in Yang et al., 2012.


This quarter we talk to Nicole Bain (MHGSA), SeniorScientist – Cytogenetics from Hunter Area PathologyService, New South Wales Australia

Q. Could you tell us a bit about your work history?I started out in research looking at tissue specific geneexpression patterns using RNA in-situ hybridisation: ofcourse now you would just use expression arrays. I movedinto diagnostic cytogenetics in 2001 with a keen interest inmolecular cytogenetics. In our laboratory I have been heavilyinvolved in the implementation of array technology as firstline testing for postnatal referrals of developmental delay and intellectual handicap. We are starting to get into prenatalsamples, however I believe you need to establish a goodlevel of experience in the array platform on postnatalsamples before venturing into the prenatal setting.

How long have you been running BlueGnome’splatform?We first started using BlueGnome’s Cytochip platform in2006-2007 on 1Mb BAC arrays. In 2007 we performedapproximately 40 postnatal arrays, this number has steadilyincreased to approximately 1400 postnatal cases in 2011,and nearly 200 foetal demise samples in 2011.

You mentioned that you’re starting to use prenatalsamples, which prenatal referrals are you considering for investigation on the arrays?We are currently running a pilot study to investigate howbest to implement array testing in the prenatal setting.Currently the prenatal microarray pilot study is restricted to referrals with foetal abnormality on ultrasound or MRI.Referrals for increased risk by triple screen test, AMA,patient anxiety, increased NT are not recommended formicroarray at this time.

Why did you feel the need to develop a specific designfor prenatal cases and not simply use the ISCA array? The ISCA design is targeted for referrals of developmentaldelay and intellectual handicap, as yet there is no ISCAconsensus on what should be put on a prenatal array.

There were two main things to consider in the design of the array, firstly what information did we want from the array and secondly how did we want our array to performtechnically. In our case, consultation and discussion with our clinicians led to the decision to remove some of theregions (currently on the ISCA design) which may causeadditional patient anxiety and are unlikely to be relevant to the current clinical presentation for example genesassociated with late onset diseases.

From a technical perspective we wanted the array to be as robust as possible and try to limit the number of single probe calls due to technical artefacts. To do thiswe consulted with BlueGnome for a loose backbone of duplicated probes to ensure an accurate result and to eliminate single probe noise, and increased density ofprobes in regions of known significance. Of course our

Interview with Nicole Bain

ideas about what should be on a prenatal will likely change as more labs start implementing the technology on prenatalreferrals.

How are you planning to report variants of unknownsignificance (VOUS) – what procedures do you have inplace for counselling patients in this event?VOUS are an inevitable fact of performing arrays. Pre-testcounselling needs to spell out the possibility that they mayarise. Parental samples must accompany the prenatal sampleso they can be tested to determine whether the VOUS isfamilial or not.

Are you planning to culture samples or are you usingdirectly extracted DNA samples?At the moment we are using cultured cells, but eventually we plan to use uncultured samples.

CytoChip Focus publications can be found in our new publications booklet:

http://www.cambridgebluegnome.com/uploads/assets/publics/3499/original/CytoChip_Focus_pub_booklet_May_2012.pdf?1339423349


We seem to have been thinking and talking about gettinginto video for quite a while now, and finally, over the lastcouple of months, we have had something to show you.

The release of BlueFuse Multi v3.0 spurred on the productionof instructional videos for installing and using the new versionof the software. We now have a video Installation guidewhich shows you how to install BlueFuse Multi in Classicmode, a Quickstart guide, which takes you on the shortestroute from microarray image to viewable results, and moredetailed Walkthrough guides for each of our main applicationareas. The Walkthrough guides are available from thecustomer area of our website and also available directlywithin the BlueFuse Multi software, through the Help menu. We hope to increase our portfolio with a number of How to’s, for using different tools in the software in the near future.

More recently we have produced some short promotional videos for 24sure, mostly with regard to the recent Yang et al publication,these have joined our original 24sure explanation video and been uploaded to YouTube (search 24sure on www.youtube.com).

See our new BlueGnome TV page www.cambridgebluegnome.com/showvideos

Julie’s news

Please could you remember to send your emails to the correct address to ensure a timely responseand so that we can file them appropriately. Our email addresses are listed below.

Orders and [email protected]

Finance related [email protected]

Technical [email protected]

For anything [email protected]

We’ve recently set up a twitter account and will beusing it get our latest news and events into themarket place. Our tweets are also displayed onwww.cambridgebluegnome.comJulie Coteman

@BlueGnomeLtd

If you’ve got some news of your own that you would like us to share, contact SallyCartwright [email protected]

See you at:

British Society for Human GeneticsWarwick, UKSeptember 17th - 19th 2012

Human Genetics Society of AustralasiaCanberra, AustraliaJuly 22nd - 25th 2012

CCMCChicago, USAAugust 6 - 7th, 2012

Movies

BlueGnomeCPC4, Capital ParkFulbournCambridgeCB21 5XEUnited Kingdomtel: +44 (0) 1223 885900 fax: +44 (0) 1223 885949email: [email protected]: www.cytochip.com


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