Simons Foundation and WuXi NextCODE Put World's Largest Autism Dataset Online to Spur New Era of Massive Genomics Research

Simons Foundation and WuXi NextCODE Put World's Largest Autism Dataset Online to Spur New Era of Massive Genomics Research

The Simons Simplex Collection is now accessible in the cloud with WuXi NextCODE clinical discovery analytics, uniting the genome and the internet for real-time queries and collaboration

- Comprising 10,000 exomes from families with one child with an autism spectrum disorder, the SSC is the largest dataset ever to be made fully usable over an ordinary internet connection

- SSC data can instantly be used in tandem with other major datasets around the world, as a standard reference and the hub for autism genomics research of unprecedented scale

SHANGHAI and REYKJAVIK, Iceland and CAMBRIDGE, Mass. and NEW YORK, March 10, 2016 /PRNewswire/ -- WuXi NextCODE, the global genomic information and precision medicine company, and the Simons Foundation today announced that the Simons Simplex Collection (SSC) is now accessible on WuXi NextCODE's integrated cloud-based database, interpretation and discovery system, the WuXi NextCODE Exchange. The WuXi NextCODE SSC portal has been inaugurated by autism researchers from seventeen leading institutions from the US, Canada, China, France, Iceland, Austria, Ireland, Brazil and Qatar, and from today will be open to researchers worldwide. Those interested can apply for training and access via the WuXi NextCODE SSC signup or by writing tocollections@simonsfoundation.org.

The SSC comprises genomic sequence and detailed clinical phenotypic data from nearly 2,600 families with one child with an autism spectrum disorder (ASD) and unaffected parents and siblings. It is a fundamental resource for advancing the understanding of ASDs and one of the largest focused collections of genome sequence data anywhere. The computational efficiency of WuXi NextCODE's database architecture makes it possible to utilize data of this scale online. SSC users can now directly interrogate individual genomes, families, or the entire collection using WuXi NextCODE's integrated clinical discovery tools. They can also tap into both GATK and FreeBayes variant calls for all samples; view findings with always-on visualizations backed by normalized global reference data; and collaborate with colleagues, all without having to move or download the data files. The data is stored in WuXi NextCODE's elastically scalable, HIPAA-compliant cloud powered by DNAnexus.

"The SSC was conceived of and has succeeded as a large-scale, open-access discovery engine. We are glad to now be partnering with WuXi NextCODE to realize this next phase in the collection's potential by making it directly accessible to the autism community worldwide," said Dr. Louis Reichardt, Director of the Simons Foundation Autism Research Initiative (SFARI). "And because it is now accessible online, the SSC can serve as the hub of a network of other major autism datasets and virtual cohorts of ever greater power. We invite everyone in the field to take advantage of this new resource."

"We are thrilled and proud to be working with the Simons Foundation to inaugurate what we see as a new era of global collaboration to better understand, diagnose and address ASDs," said Hannes Smarason, COO of WuXi NextCODE. "Putting the SSC on the Exchange is a landmark in creating a working internet of DNA, and it is appropriate that it should address autism. Unravelling its complexity demands the creation of truly vast datasets, and we look forward to working with the Foundation and the autism community to refine this resource, bring in whole genome data, and continue to expand the scale, scope and reach of the SSC in pursuit of this goal."

"This is a game-changer and we are already using the WuXi NextCODE SSC portal to validate and extend new discoveries and confirm clinical diagnoses," said Dr. Timothy Yu, a clinician and assistant professor of neurology at Boston Children's Hospital. "This is the way the investment in big genomics is going to deliver on its potential to accelerate our understanding of autism and many other complex conditions. Since we and a growing number of our collaborators have our research and diagnostic data in GOR format, we are already seeing the impact of big virtual cohorts for rapidly advancing the field and are inviting our collaborators to do the same."

The SSC comprises whole-exome sequence data and more than 2000 phenotypic variables for some 2,600 ASD probands and their parents and unaffected siblings. Among the portal's features are:

·       All SFARIGene and other major ASD gene and variants lists

·       All major public reference datasets

·       Instant visualization of raw BAM sequence reads

·       Variant aggregation to power statistical association of rare variants

·       De novo, paralog detection

·       Carrier analysis

·       Toggle filters for predicted variant impact and allele frequencies

·       Histographic selectors and report builders for phenotype definition

·       Import and merge functionality to incorporate external datasets

波士頓華埠社區中心猴年新春大吉 籌款數額破30萬元大關

波士頓華埠社區中心行政主任李隆華（左一），董事會主席鍾潔姿
（右二）請嘉賓上台表揚得獎個人。（周菊子攝）

(Boston Orange 周菊子報導)波士頓華埠社區中心（BCNC）昨（9）日公佈，第28屆農曆新年聯歡宴，籌款打破歷年紀錄，總額達30萬7000元。

波士頓華埠社區中心3月4日晚在必珠街的喜臨門大酒樓舉辦這場聯歡會，藉出售席券，做現場及無聲拍賣來籌款，並在會中表揚了四名有成就，貢獻者，安排了楊書旺的四川變臉，Vivian Lo的小提琴獨奏等表演娛賓。

麻州財政廳廳長高柏珂（Deb Goldberg），波士頓市議會議長吳弭（Michelle Wu），昆士市市議員梁秀婷等嘉賓應邀出席，與550多名賓客同歡。

三名麻州眾議員黃子安，陳德基，麥家威（Aaron Michlewitz）聯名簽署了一份表揚狀，稱許波士頓華埠社區中心為社會所做貢獻。波士頓市長馬丁華殊（Martin Walsh）也捐出四人一組的拜訪，合影機會做義賣品，以試支持。

BCNC主席鍾潔姿（右一）歡迎國泰銀行高管白勝德（右二）等人到會。

還有刻正競選轄區包括華埠麻州參議員席位的黃子瑜，到會場拜票。康可鎮鎮議員伍甘澍出席支持。

波士頓華埠社區中心董事會董事長鍾潔姿，行政主任李隆華在會中報喜訊，指出BCNC已連續兩年獲得慈善導航（Charity Navigator）的四星評等，導星（Guidestar）根據財務結果及管理良善與否衡量的金級平等，將繼續在強調家庭的框架下，為移民服務。

他們也說明，該中心去年的擴展成績令人興奮，進駐了昆士市，為當地居民及家庭提供服務，今年更在昆士市設立了永久據點，辦理英語班，該中心已連續三年獲得麻州政府的成人教育服務最高評等。在培訓青年領袖，輔助升讀大專院校，支援移民家庭上，該中心的服務都辦得很成功，他們還和波士頓城市學院（Urban College of Boston）合作，辦了以中文教授，可獲大專學分的課程。

麻州財政廳廳長高柏珂恭賀BCNC
猴年新春快樂。（BCNC提供）

當晚在會上獲表揚的四人，分別為周志華（譯音，Chi Wan Chow）獲塔芙茨醫療中心堅強家庭獎，張紹龍（譯音，ShaoLong Zhan）華人醫務中心成人學生獎，李菲利（譯音，Felix Li）獲哈佛格林健保青年領袖獎，譚艾倫（譯音，Ellen Tang）獲美國銀行輔導者獎。

波士頓市議會議長吳弭（右）致詞。（周菊子攝）

昆市議員梁秀婷（右）致詞。（周菊子攝）

康可鎮議員伍甘澍（中）出席BCNC農曆新年慶祝會。
（周菊子攝）

刻正競選麻州參議員的黃子瑜（左）到BCNC新年慶祝會
拜會，遇昆士市議員梁秀婷（右）。（周菊子攝）

波士頓宣佈成立小企業發展辦公室提供一站式服務

波士頓市長馬丁華殊（前左），經濟發展長巴洛斯（前右一），范文南
（前右二），狄倫（前右三）等人在市府大樓前宣佈“小企業計劃”。
（周菊子攝）

(Boston Orange)波士頓市府3月9日中午推出“小企業計劃”，宣佈成立“小企業發展辦公室（Office of Small Business Development）”，期以藉由整合市府部門，提供一站式服務，尤其要輔導婦女及少數族裔經營的小企業發展更成功。

聯邦小企業行政局專員伍少武（右起），波市企業發展專
員甄碧鳳，麻州住宅及經濟發展助理部長范文南，企業家
盧桂齡等人出席波士頓市輔小企業計劃發佈會。
（周菊子攝）

波士頓市長馬丁華殊(Martin Walsh)，經濟發展長巴洛斯（John Barros），鄰里發展局局長狄倫（Sheila Dillon）和應邀出任社區顧問的麻州企業發展助理部長范文南（Nam Pham）等人，9日在市府大樓前宣布了把鄰里發展局（DND）麾下，業務包括市內20個主街計畫的企業發展辦公室，劃歸市長經濟發展辦公室，交由巴洛斯掌管的這一市府結構變動，強調今後小企業與市府打交道，程序更簡化，援助更多。

巴洛斯（左）將主管新設的小企業發展辦公室，統領劃歸
該部門的甄碧鳳等工作人員。（周菊子攝）

波市府的“小企業計劃”是由波市府鄰里發展局，經濟發展辦公室和未來街(Next Street)，麻州經濟(Mass Economics)等機構合作，邀請了范文南等34名來自業界，婦女及少數族裔企業東主，初創企業等小企業圈人士擔任顧問，調查研究七個月後制定。其中一項重要成果是做了一份“波士頓市小企業概況”報告，蒐集了市內所有的小企業，輔助企業組織，資金提供機構等數據資料。

這些資料包括，波士頓市內現有約40,000家小企業，每年營業額共約150億元，為波士頓市創造了17萬個工作機會。其中少數族裔擁有的企業約佔32%，營業額27億元，聘用32,000多名員工。

這些小企業有85%都屬於微型企業，聘用員工人數少於10人，年營業額低於50萬元。但在波士頓市私有盈利企業中工作的員工，有44%都是在小企業中工作。

”小企業計劃“的34名顧問中，包括系列創業家張紹遠，
美美接廚房餐廳東主Mei Li。

37%的波士頓市私有營利企業營業額，來自小企業。

波士頓市的這首份“小企業計劃”，還列出了小企業在經營生態中的需求，以及市府的因應策略，包括設立小企業中心，供小企業專用的311熱線，新的小企業網站，整合資金提供者資料，支持替代性資金提供者的發展及設立，以增加小企業取得資金渠道。

波市府還將推出“錨委員會“和大機構合作，以支持影響力高的小企業，推出“波士頓到波士頓”脈絡網，以增加向本地小企業採購數量，為小餐館、零售商設立一個新的輔導網項目，並針對有高成長潛力小企業，提供一對一輔導。

MAYOR WALSH ANNOUNCES CITY OF BOSTON GRANTS FOR DACA/DAPA OUTREACH AND EDUCATION

MAYOR WALSH ANNOUNCES CITY OF BOSTON GRANTS FOR DACA/DAPA OUTREACH AND EDUCATION

BOSTON - The funds come from an $80,000 match grant from the Emma Lazarus II Fund of the Open Society Foundations, with matching funds of $25,000 each from four local foundations: the Boston Foundation, the Fish Family Foundation, theHerman and Frieda L. Miller Foundation, and the Hyams Foundation. "I am excited that these grants will make the Boston DACA/DAPA Outreach Initiative possible," said Mayor Walsh. "I have supported President Obama's sensible executive actions on immigration, and I am very pleased to have the opportunity to expand upon our efforts to ensure that Boston families have the information and assistance that they need to continue to contribute to our great City." "This funding provides much needed support for a priority in many of our immigrant communities," said Alejandra St. Guillen, Director of the Mayor's Office of New Bostonians. "Many of our community organization partners have already been doing some work on this issue. Now, we have an opportunity to build a structure to coordinate and to increase DACA and DAPA outreach, education, and screening services." "Nobody understands the benefits immigrants bring-economically, culturally and socially-better than the cities where they live," said Ken Zimmerman, director of U.S. Programs at the Open Society Foundations. "We are pleased to partner with the city of Boston, which is taking a leadership role in informing its longstanding immigrant communities about protections available to them under the law-efforts which will help them further contribute to the life of the city. We also applaud the local foundations for their involvement, and look forward to working with them to help  strengthen the infrastructure of support for immigrant communities in Boston over the long run." "The Hyams Foundation has had a long-standing commitment to Boston's diverse immigrant communities," said Beth Smith, executive director of the Hyams Foundation. "Along with our three local funding colleagues, we are pleased to support the Mayor's Office of New Bostonians' response to a national funding opportunity while remaining committed to broader and more permanent immigration reform that allows for these vital populations to continue contributing to our city. We appreciate Open Society Foundations' partnership in this important work as well as the Boston Foundation, Miller Foundation, and Fish Family Foundation." The DACA/DAPA Outreach Initiative will consist of a program coordinator in the Mayor's Office of New Bostonians (MONB) and provide $100,000 in grants to 21 community organizations to inform Boston's immigrant communities, provide eligibility screenings, assist with applications when they become available, and prevent scams. These community organizations will convene onMarch 31, 2016 to develop and coordinate a plan of action. The following organizations will be partnering with the City of Boston on this initiative: Action for Boston Community Development (ABCD) Agencia ALPHA Asian American Civic Association Brazilian Women's Group Brazilian Worker Center Catholic Charities of Boston Centro Presente Chelsea Collaborative Dominican Development Center East Boston Ecumenical Community Council (EBECC) Gilbert Albert Community Center Immigrant Family Services Institute Irish International Immigrant Center Latinos Unidos en Massachusetts (LUMA) Massachusetts Immigrant and Refugee Advocacy Coalition (MIRA) Massachusetts Law Reform Institute (MLRI) Political Asylum/Immigration Representation Project (PAIR) St. Mark's Community Education Program Students Immigration Movement Tabernacle Baptist Congregation True Alliance Center After President Obama's announcement of executive actions on immigration in November 2014, MONB launched a "Know the Facts" Campaign which involved coordinating community organizations, staffing an information hotline, publishing materials, giving community presentations, and holding a screening clinic event to educate the public, serve those who might benefit, and prevent scams. MONB has also co-hosted events assisting those eligible for the 2012 version of DACA with their applications and renewals. In May 2015, Mayor Walsh wrote an op-ed and held press conference at Faneuil Hall to further voice the importance of expanded DACA and DAPA to Boston's eligible immigrant communities. On Tuesday, March 8, 2016, Mayor Walsh joined 117 mayors, county executives, and local governments, as well as the U.S. Conference of Mayors and the National League of Cities in submitting an amicus brief to the U.S. Supreme Court in support of the executive actions on immigration in United States v. Texas, the lawsuit that has led to a preliminary injunction preventing the implementation expanded DACA and DAPA.

B.A.A. Announces Native American Running Partnership with Harvard University

B.A.A. Announces Native American Running  Partnership with Harvard University

Panel discussion and speaker series among events set to recognize Native American traditions during Boston Marathon weekend.

BOSTON – Working closely with Harvard University, the Peabody Museum of Archaeology & Ethnology, and the Harvard University Native American Program, the Boston Athletic Association is pleased to announce that numerous events exploring the history and importance of Native American running traditions will be featured during Boston Marathon weekend this year. Past, present, and future Native American running culture will be explored leading up to the 120th Boston Marathon, to be held on Monday, April 18, 2016.

The free, multi-day event, which is titled Native American Running: Culture, Health, Sport, will not only explore the history and importance of Native American running traditions, but will also present efforts to support and encourage running in Native American communities.

"We are proud and honored to work with our friends at Harvard University to celebrate and showcase Native American running, both here on the roads to Boston and beyond,” said Tom Grilk, Executive Director of the B.A.A. “The events planned for Boston Marathon weekend will be both inspirational and educational, exploring all facets of Native culture through running and sport.”

Kicking off the celebration will be a Native American Running Conference at Harvard University on Friday, April 15, followed by two panel discussions at the John Hancock Sports & Fitness Expo on Saturday, April 16, from 11:00 a.m. to 1:00 p.m. at the Hynes Convention Center. Both events are free and open to the public.

"Every culture runs, but Native American running traditions are special. These events will explore and honor Native American running in all its rich diversity, from its origins to the present, including in the Boston Marathon,” said Daniel E. Lieberman, Harvard University’s Edwin M. Lerner II Professor of Biological Sciences. A leading expert in the evolutionary benefits of running for both Native American cultures and the general population, Lieberman will participate in both the panel discussion and expo series on Boston Marathon weekend. “We have much to learn about Native American running traditions, and we need them more than ever."

Among the distinguished guests also participating are Billy Mills, a member of the Oglala Lakota (Sioux) Nation, the 1964 Olympic gold medalist over 10,000 meters, and a Native American leader, as well as athletes from the Tarahumara indigenous people of Mexico’s Copper Canyons. Representing the Tarahumara will be Arnulfo Quimare, one of the most accomplished ultra-marathoners in history, and Irma Chavez-Cruz. Both Quimare and Chavez-Cruz will race the 120th Boston Marathon.

Chris McDougall, author of the bestselling book, Born to Run: A Hidden Tribe, Superathletes, and the Greatest Race the World Has Never Seen, which chronicles the Tarahumara, will also be on hand to participate in panel and expo discussions.

Other scheduled participants include 1986 Boston Marathon champion Rob de Castella, a leader of the Indigenous Marathon Foundation in Australia; three-time Boston Marathon runner-up Patti Dillon, a Micmac Indian and the first American woman ever to break 2:30 in the marathon; Chris Sockalexis, a Penobscot Tribal Historic Preservation Officer and relative of Olympian and marathon great Andrew Sockalexis; and Mickey Mahaffey, a guide, cultural consultant, race organizer, and researcher of indigenous Mexican tribes.

This April, the B.A.A. will also celebrate two native champions: Ellison "Tarzan" Brown, the 1936 and 1939 champion, as well as Thomas Longboat, the 1907 Boston Marathon victor. The 2016 Boston Marathon marks the 80th anniversary of “Tarzan” Brown’s 1936 victory, the iconic race which is said to have led to the naming of “Heartbreak Hill.” The B.A.A. also recognizes Andrew Sockalexis, a member of the Penobscot of Maine who placed second in 1912 and 1913.

Connecting the week’s celebration of Native running traditions to the Patriots’ Day race, representatives from the Tarahumara indigenous people will compete in the 120th Boston Marathon. In addition, members of Wings of America and Running Strong for American Indian Youth (a charity which helps American Indians meet their immediate survival needs while creating opportunities for self-sufficiency and self-esteem in American Indian youth), as well as Rob De Castella’s Indigenous Marathon Foundation, will also race from Hopkinton to Boston.

"Generations of Native runners have competed and excelled at various levels across the nation.  The teams of Native runners participating this year continue to share and represent these strong cultural running traditions,” said Shelly C. Lowe, Executive Director of the Harvard University Native American Program. “We are absolutely delighted to shine a national light on Native runners this year as we join the B.A.A. in celebrating the accomplishments of Tarzan Brown, Thomas Longboat, and Andrew Sockalexis.”

A youth team from Wings of America has been invited to compete in the B.A.A. Relay Challenge on Saturday, April 16, extending the Native American tradition to one of Boston Marathon weekend’s most fun-filled events. Wings of America uses running as a catalyst to empower American Indian and Alaskan Native youth to take pride in themselves and their cultural identity, leading to increased self-esteem, health and wellness, leadership, and hope, balance, and harmony.

Native American tradition is intertwined with the roads leading to the Boston Marathon finish line. In 1907, Canadian Thomas Longboat, of the Onondaga Six Nations, won the Boston Marathon in a course-record time of 2:24:24. Nearly three decades later, Narragansett tribal member Ellison “Tarzan” Brown triumphed in 1936 and 1939, establishing himself as one of the most dominant Boston Marathon champions of the decade. Andrew Sockalexis, a member of the Penobscot of Maine, placed second in 1912 and 1913.

The entire running community is welcome to connect and experience the Native American running traditions at both the Native American Running Conference at Harvard University on Friday, April 15, and at the speaker series at the John Hancock Sports & Fitness Expo on Saturday, April 16. Both events are free and open to the public.

More information can be found via the Boston Athletic Association’s website, www.BAA.org, as well as at the Peabody Museum of Archaeology and Ethnology’s website, www.peabody.harvard.edu/native-american-running.

U.S. DOT Issues Guidance for States to ‘Repurpose’ Roughly $2 Billion in Unused Earmarks

U.S. DOT Issues Guidance for States to ‘Repurpose’ Roughly $2 Billion in Unused Earmarks

WASHINGTON – U.S. Secretary of Transportation Anthony Foxx announced that roughly $2 billion in previously unused earmarks can be put back to work to support infrastructure projects across the country, as described in new guidance from the Federal Highway Administration.  

This announcement builds on actions that began in the earliest days of the Obama Administration, when the President worked together with Congress to change the way that business is done in Washington by increasing transparency and accountability for the way that taxpayer dollars are spent – including through reforms that moved us away from the practice of directing funding through earmarks. 

“This is a tremendous opportunity for state and local governments to work together to identify their needs heading into the next 30 years,” said Secretary Foxx.  “I encourage these leaders to identify innovative projects that reconnect their communities and increase access to jobs, education, and basic services.”

Today’s guidance implements a provision in the Consolidated Appropriations Act 2016, which gave states the option of repurposing certain earmarked funds if the original earmark was over 10 years old and if less than 10 percent of project funds had been obligated, or if the project is closed.  Through the end of FY 2016, states have the option of re-designating these dollars to other projects within 50 miles of the originally intended use.  A list of earmarks that may be eligible for repurposing is available here: http://www.fhwa.dot.gov/cfo/earmarkrepurposing.

The guidance describes the process by which state Departments of Transportation issue such notifications, making the funds immediately available for use.  Once a state elects to repurpose funds, it will have until the end of FY 2019 to obligate the funds.

“Today’s action is an important reminder of how far we’ve come over the course of this Administration,” said Federal Highway Administrator Gregory Nadeau.  “By providing a path to put nearly two billion stranded dollars to work, we have an important opportunity to support infrastructure projects across the country while at the same time clearing a legacy backlog and promoting good government.  Instead of sitting idle, these funds can help keep drivers safe and provide opportunities for communities nationwide.”

This action also builds on a range of steps taken by USDOT in recent weeks to make billions of Federal dollars available for communities across the country to improve our infrastructure and economy, foster innovation, and create access to opportunity.  And prospective applicants should be aware of a number of important, open funding opportunities.  For example, USDOT is currently accepting applications for: $800 million available through a newFASTLANE grant program, to fund critical freight and highway projects across the country; $500 million for transportation projects across the country under an eighth round of the highly successful Transportation Investment Generating Economic Recovery (TIGER) competitive grant program; and up to $72.5 million available this year through the University Transportation Centers (UTC) to consortia developing innovative transportation solutions – and that can, for the first time, include two-year institutions of higher learning.  

Today’s action also builds on a similar action in August 2012, when USDOT made over $470 million in unspent earmarks immediately available to states for projects that create jobs and help improve transportation across the country.