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About the MacArthur Lab

We are a tight-knit research group jointly based as Massachusetts General Hospital and the Broad Institute of Harvard and MIT, and leveraging the largest genomic data sets in the world and cutting-edge analysis methods to make sense of human genetic variation. We’re committed to open data and open-source code, as well as experimenting with new methods of communication. Working with us is a chance to learn from experts in computational biology, large-scale genomics, variant interpretation, software development and clinical genomics, as well as to make a difference to the lives of hundreds of families affected by rare diseases.


Associate Computational Biologist II

Despite recent advances in genomic technologies, the majority of families affected by rare genetic diseases still cannot be given a precise molecular diagnosis. We are seeking a creative and self-motivated candidate to play a key role in developing computational methods to improve the diagnosis of rare disease. These tools will be applied to thousands of families affected by rare diseases, many of whom have been waiting for many years for a formal genetic diagnosis for their disease, and used to make new discoveries that can then be clinically validated and returned to families.

In this role you will design and implement code to analyze RNA, genome, and exome sequencing data at scale in three essential areas of interest:

  1. Identifying unusual splicing and gene expression in RNA-seq (transcriptome) data to identify genetic causes of previously unsolved rare disease cases
  2. Identifying structural variants in whole-genome sequencing data
  3. Accurately detecting sequence repeat expansions in genome and exome data

Our group is an interdisciplinary team of academic trainees, computational biologists, software developers and other personnel, engaged in the design, development, and deployment of cutting-edge genomic technologies at exceptional scale to characterize and interpret the impact of human genetic variation. As part of our methods development group, you will have the opportunity to make substantial contributions to patients and families affected by rare disease, as well as to participate in the vibrant research environment at the Broad Institute, with its close links to MIT, Harvard, and the Harvard-affiliated hospitals across Boston. You will have access to data sets of unprecedented scale, including genome and exome sequencing data from hundreds of thousands of reference individuals and thousands of rare disease families, and to colleagues with deep expertise in genetics, computational biology, software development, and machine learning.

The responsibilities of this role align closely with the mission of the Broad to transform medicine and human health through cross-disciplinary collaboration and the development of pioneering technologies to analyze scientific data on an unprecedented scale.

Primary Responsibilities:

    • Implementing, benchmarking, and optimizing existing computational algorithms to address research questions and analysis objectives
    • Writing new algorithms to handle data in cases where no satisfactory methods exist
    • Regularly contributing code to our public GitHub repository and participating in team-based code review
    • Monitoring and assessing current, relevant scientific literature related to the group’s analysis aims, in order to understand emerging practices and to ensure the group continues to employ optimal methods
    • Initiating consultations with scientists, software engineers, and mathematicians within and external to the Broad with relevant specific expertise in the course of evaluating existing methods and developing novel ones
    • Soliciting and implementing software feature requests from critical stakeholders, including variant analysts within the group, fellow members of the software engineering and methods development team, external clinical collaborators, and other end-users
    • Designing clear, appealing, and accessible figures, readouts, and/or user interfaces that provide analytical insight into the data for clinical researchers using our online analysis platform; and implementing an automatic workflow for producing such reports
    • Presenting results at regular intervals at lab and project team meetings, including meetings with external collaborators as well as institute, national, and/or international conferences as appropriate
    • Contributing code, figures, and text to team presentations and publications, including, as appropriate, leading and coordinating manuscript writing for the candidate’s first-author publications

Characteristics and Qualifications

The role will require an independent and highly motivated candidate with the ambition to establish a significant body of code that advances the discovery of the genetic causes of rare disease.

You will have an interest in developing domain expertise in computational methods for analyzing next-generation sequencing data, as well as an interest in the technical aspects of deploying these methods at scale.

We are looking for someone who:

    • Is able to write clean, efficient, robust, and usable code, with demonstrated proficiency in one of the following: Linux, Perl, Python, Java, C++, Matlab, or R, with a preference towards Linux, Python, and R
    • Has a BS or MS degree and 0-2 years experience in computer science, engineering, physics, mathematics, statistics, biology, or related fields
    • Has demonstrated experience in quantitative (statistical, mathematical, computational) research with large data sets; skill and experience with statistical analysis and/or computational biology is strongly preferred
    • Has fluency with human genetics and next-generation sequencing data; ideally will have prior experience with algorithms relevant to RNA-Seq analysis
    • Exhibits strong initiative and the ability to take ownership of assigned tasks and projects
    • Listens, communicates, and collaborates well with team members, clinicians, software developers, and research scientists
    • Demonstrates excellent written and oral presentation skills
    • Manages time well and is able to respond to shifting priorities in a fast-paced and rapidly changing environment

Please apply via Broad Institute careers site.

Clinical Genomic Variant Analyst: Rare Disease Group

The Broad Institute Center for Mendelian Genomics (CMG) is an NIH-funded collaborative venture, co-directed by Drs. Heidi Rehm and Daniel MacArthur, to discover new genes underlying Mendelian diseases; to develop collaborative networks of investigators to facilitate gene discovery, validation and follow-­up; and to generate new methods for gene discovery applicable across a wide spectrum of rare disorders. Our CMG (cmg.broadinstitute.org) performs exome or genome sequencing on thousands of unsolved Mendelian cases and unaffected family members. Our team has also recently launched the Rare Genomes Project (https://raregenomes.org/), a direct-to-patient genome sequencing initiative. Our mission is to partner directly with patients, families, advocates, and clinicians to accelerate the rate of rare disease diagnosis and increase patients’ access to genomic research.

We are searching for an enthusiastic analyst to interpret rare disease exomes and genomes in order to identify causal candidate genes and variants at the CMG and RGP. This will involve using our in-house exome analysis software to analyze and interpret genetic variation in families to diagnose patients with rare disease. The analyst will also manage and coordinate activities for their respective rare disease cohorts, working closely with a set of clinical collaborators from around the world. In addition, he/she will work in close collaboration with other members of our team, which includes analysts, genetic counselors, clinicians, computational biologists, software engineers, and project managers.

The candidate should have a strong background in genetics or related discipline, have fluency in human disease genetics, have good attention to detail and be able to adapt quickly and be part of a cross-functional team in a rapidly changing environment.

This is an opportunity to work at the interface between large-scale genomics, informatics, and disease genetics, and to have an impact on the lives of hundreds of families affected by rare, severe diseases.

Primary Responsibilities:

    • Directly analyze exome and genome data for identification of disease-causing variants, using existing and newly-developed analysis tools through in-house software (seqr), for hundreds of rare disease families.
    • Present results and progress at regular team and other Broad Institute meetings.
    • Perform clinical correlation of gene/variant with patient phenotype, scientific literature review, and variant classification using ACMG criteria.
    • Manage interactions with several research and clinical collaborators to facilitate information exchange to help diagnose cases and to confirm new candidate variants and genes.
    • Participate in education and mentorship of other analysis staff and collaborators through direct interaction and presentations.
    • Involvement in abstract, figure, and manuscript preparation and submission, and presentations at local or national professional conferences.

Characteristics and Qualifications:

    • Undergraduate degree in biology, genetics, or related field OR Master’s degree in Genetic Counseling/Human Genetics from an ABGC accredited Program OR other relevant discipline or equivalent experience required
    • Experience in rare disease analysis and variant interpretation
    • Basic understanding of human genetics and next-generation DNA sequencing
    • Familiarity with genomic data, tools and databases
    • Demonstrated attention to detail and analytical skills
    • Excellent communication skills
    • Excellent organization and time management skills
    • Highly collaborative and able to work well in a team
    • Programming experience not required, but some experience in Python, R, and Unix would be advantageous

Please apply via Broad Institute careers site.

Clinical Project Coordinator: Rare Disease Group

The Broad Institute’s Rare Disease Group is focused on applying genomic technologies to diagnose families affected by rare genetic diseases. To assist with these efforts, we are seeking an organized and motivated Clinical Project Coordinator (CPC) to work on the Rare Genomes Project (RGP) (http://www.raregenomes.org) within the Broad Institute’s Rare Disease Group. This project is led by Drs. Daniel MacArthur and Heidi Rehm.

The RGP is our direct-to-patient genome sequencing initiative. Our mission is to partner directly with patients, families, advocates, and clinicians, to accelerate the rate of rare disease diagnosis and increase patients’ access to genomic research. The CPC will ensure that these efforts run smoothly and effectively.

In this role, your primary responsibility will be to interact with the families that participate in our project. The successful candidate will obtain families’ consent to participate and ensure that they have all materials needed to be an active and engaged participant. Due to time zones and to accommodate family schedules, we are particularly interested in candidates who have flexibility to be able to periodically take calls from participants during evenings or weekends when needed. You will work with a diverse team of physicians, genetic counselors, analysts, software engineers, computational biologists, and investigators, among others on our team, to help rare disease families from around the country. The ideal candidate for this position is detail-oriented, comfortable talking with patients and families, enthusiastic about clinical research, and has a desire to continuously improve processes.

Primary Responsibilities:

    • Consent project participants through phone and video interactions.
    • Prepare and execute required consent and other regulatory documentation.
    • Schedule appointments with participating families who have signed up to participate online.
    • Track samples and data collected and generated as part of the project.
    • Obtain, compile, and enter demographic, clinical, and necessary study data into a database.
    • Assist with requesting medical records from participants, extract information from their medical records, and enter information into a database.
    • Maintain confidential, accurate, and detailed study participant records.

Characteristics and Qualifications:

    • Bachelor’s Degree in a biological science and/or coursework in genetics.
    • Experience in a clinical research or other healthcare setting is preferred; prior consenting experience appreciated but not required.
    • Must be detail oriented and extremely self-motivated, with the ability to effectively manage time and prioritize workload.
    • Excellent organization, communication, and time management skills required.
    • Strong interpersonal skills with ability to effectively interact with families and all levels of staff and external contacts.
    • Ability to work both independently and as part of a multidisciplinary team in a fast-paced and challenging work environment, and respond to shifting priorities.
    • Must possess a high level of initiative.
    • Must have computer skills, including the use of Microsoft Office and Adobe Acrobat.
    • Experience working with data tracking and organization preferred.
    • Flexibility to work some atypical hours preferred.
    • Candidates who can make at least a two-year commitment preferred.

Please apply via Broad Institute careers site.

Software Engineer: Rare Disease Genomics

Join a team that’s building open-source web-based decision support tools to dramatically accelerate the pace of diagnosis for families affected by rare genetic conditions. Our platform seqr (github.com/macarthur-lab/seqr) is used by an international consortium of collaborating clinicians, researchers, and industry partners, and significantly improves their ability to search through large genetic datasets and make discoveries and diagnoses. seqr is core to our efforts both in the Rare Genomes Project (raregenomes.org) and the Broad Center for Mendelian Genomics (cmg.broadinstitute.org), and has already enabled us to provide genetic diagnoses to more than 1,000 rare disease families. We are now looking for a full-stack software engineer that will help with the next phase of this project.

Your primary responsibilities will include designing and implementing new features. This may include developing intuitive visualizations and user interfaces (using javascript, React.js), integrating new kinds of datasets, and designing new APIs and database schemas (in python and Django, elasticsearch and PostgreSQL). We welcome applications from diverse backgrounds and experience levels. Knowledge of genetics or biology is preferred but not required. Above all, the ideal candidate will have strong engineering skills, a desire to learn new domains, and the enthusiasm and ability to contribute to multiple aspects of seqr development.

Requirements:

    • BS or MS degree in Computer Science or other scientific discipline.
    • Experience delivering clear, well-designed software.
    • Interest in working with a wide variety of technologies and on diverse problems.
    • Excellent communication skills and ability to work with users.
    • Experience with web-based application development in python and javascript is required.
    • Experience with Django, React.js, Redux, SQL, elasticsearch, Google Cloud Platform and Kubernetes is preferred.
    • Familiarity with genomics and DNA sequencing data analysis is a plus.

Please apply via Broad Institute careers site.


Post-doctoral Fellows

We are looking for postdoc candidates with backgrounds in computational genomics or statistical genetics, ideally with direct experience in analyzing human sequencing data. Projects include identifying human knockouts, leveraging large human genetic data sets for drug target discovery, and improving the diagnosis of rare disease patients. Most importantly, we’re looking for people who are passionate about the translation of genomics into clinical practice, and have the right personality to work in a fast-paced and highly collaborative environment.

To apply, email Daniel with your CV.