July 2018 – Page 2 – Lablogatory

Next Generation Sequencing – Ion Torrent Semiconductor Sequencing

We’ve finally made it to the sequencing step of the NGS workflow. This post we will discuss the technology and process behind the Ion Torrent sequencing step. Next time, we will review the Illumina sequencing process.

When we left off, the final product of the clonal amplification had been prepared – Ion Sphere Particles (ISPs) covered in single stranded amplicons (hopefully all of the same amplicon). Next, control Ion Sphere Particles are added to the mix, along with sequencing primer, which is complimentary to one of the adapter sequences added back in library preparation. The primer is annealed to each of the amplicons on every ISP. This mixture of control ISPs and specimen ISPs is then loaded onto the chip. The size of the chip is determined by the number of bases needing to be sequenced. There are three different types of chips for the Personal Genome Machine (PGM) – 314, 316, 318 – and five different types for their GeneStudio S5 system (510, 520, 530, 540, 550), offering enough coverage for a single sample of a hotspot panel, all the way up to enough coverage for a specimen of exome sequencing. Each of the chips contains a top layer covered in tiny wells. Each well is just large enough to fit a single ISP. The ISP solution is loaded onto the chip, then flowed over it by centrifuging it in different directions, in order to attempt to get as many ISPs into wells as possible. The chip is then ready for sequencing.

Each well of the chip can be thought as of the smallest pH meter in the world. So before sequencing can be started, the instrument must be prepped (initialized) so that all of the reagents added to the chip are in the correct pH range. On the PGM, this takes approximately an hour and requires some hands-on steps and high quality 18MΩ water. On the GeneStudio S5, the reagents are added and the initialization is begun and, as long as everything works correctly, doesn’t require any other hands on time.

After the initialization is complete, the chip is loaded onto the instrument. The sequencing run is started and runs according to the plan prepared before the run. Thermo Fisher’s Ion Torrent uses semiconductor sequencing technology. Nucleotides are flowed over the chip one at a time. If the nucleotide is incorporated, a hydrogen ion is released. This release of hydrogen decreases the pH of the liquid surrounding the ISP. This pH change is then detected by the sensing layer beneath the well, where it is converted to a voltage change and is picked up by the software and recorded as that nucleotide. Let’s say two nucleotides in a row are incorporated (two G’s complementary to two C’s) – double the hydrogen is released, which results in double the signal, so the software will record two G’s in a row. The benefit of this type of technology is that it is fast – it only takes 15 seconds for each nucleotide flow, so a 200bp fragment can be sequenced in less than 3 hours.

ion-torrent — Image courtesy of http://www.genomics.cn/en/

rapp_small

-Sharleen Rapp, BS, MB (ASCP)^CM is a Molecular Diagnostics Coordinator in the Molecular Diagnostics Laboratory at Nebraska Medicine.

History of Generations: Baby Boomers

One of most well-known names of generations, besides perhaps Millennials, are the Baby Boomers. The Baby Boomers generation is currently the largest generation. Of all the generations, they cover the largest span of time (those born from 1946 to 1964). In large parts of the world, there was a big surge in births after the Second World War. That war had a significant influence on their values, perceptions, attitude, and approach to work.

One of the major aspects that make Baby Boomers stand out from previous generations is that this was really the first generation in which women started to work outside the home in large numbers, at least in the Western Hemisphere. This has a major influence on the home and work environment. In the United States, the children of Baby Boomers often had a latchkey around their neck so that they could go home after school without their parents being there.

Baby Boomers played a large role in shaping today’s society; they used music as a political tool, they increased focus environmental conservation, they were involved with the civil rights and women’s rights movements, and they are politically informed and outspoken. It is also the first generation in which both divorce and homosexuality became accepted. Overall, this generation is known for optimism, adaptability, having a strong work ethic, and being team-oriented.

Even though technology did not become part of daily life until Generation X, Baby Boomers witnessed enormous technological milestones, such as the first orbit around earth, landing a man on the moon, and the creation of the first nuclear power plant. All these events set the stage for later advances, and Baby Boomers are typically interested in learning how to use technology, although it does not come as natural to them as future generations. They also have tend to work longer and retire later in age, mainly because they link their self-worth to their job. In other words, their work ethic becomes their “worth ethic.” Knowing this when working with them is important, as they appreciate recognition in forms of awards, title changes, and public acknowledgement for their contributions.

Because this generation spans such a long time (and because some Boomers had children later in life due to second and third marriages), Baby Boomers are parents to both Generation X and Generation Y. There is a lot to learn from this generation, so next time you work with one ask for some of their insights and understanding. This generation makes great mentors, especially because they are likely to have children of mentee age.

lotte-small

-Lotte Mulder earned her Master’s of Education from the Harvard Graduate School of Education in 2013, where she focused on Leadership and Group Development. She’s currently working toward a PhD in Organizational Leadership. At ASCP, Lotte designs and facilitates the ASCP Leadership Institute, an online leadership certificate program. She has also built ASCP’s first patient ambassador program, called Patient Champions, which leverages patient stories as they relate to the value of the lab.

Here is an interesting fact: there are two sub-sets of Baby Boomers. The first ones are the “Save-The-World Revolutionaries” of the ’60s and ’70s. The second set of Boomers are the career climbers, the yuppies, of the ’70s/’80s. The most profound characteristic of a Baby Boomer is their work ethic. They identify with their job, profession, or their career. So much so, that this generation has remained in the workforce beyond the age of 70.

In a lot of ways, I’m the typical Baby Boomer woman. I married the first time just before I was 20 years old. Divorced in my early 30’s and moved forward in my career because that’s what the “Boomer Women” did. They worked inside and outside of the home.

As a laboratory professional that left the bench many decades ago, and now working in the field of Organizational Leadership and Development, I am approaching the age of 70. I’m starting to realize my retirement day is closer than I’d like. Like others of my generation, this concerns me because I am defined by my career! The thought of not working left me searching for my identity so much that I started seeing a therapist last year. I was, and am fortunate to work for an incredible organization that doesn’t judge one by their age. They look at the skills and competencies one brings to the table. I’m consciously working on succession planning so that my institutional knowledge remains with the organization and its people. It also helps to have two gifted professionals who wanted to learn from me and grow. Then it takes a manager like mine who supports me through this often painful process. I am blessed with that kind of support. Sometimes the work ethic equals “worth ethic” in the body, mind, and spirit of a Baby Boomer, which is something to keep in mind when working with this generation.

Stakenas-small

-Catherine Stakenas, MA, is the Senior Director of Organizational Leadership and Development and Performance Management at ASCP. She is certified in the use and interpretation of 28 self-assessment instruments and has designed and taught masters and doctoral level students.

Microbiology Case Study: A 60 Year Old Female with Right Ear Pain

Case History

60 year old female presents to the emergency department with increased pain in her right ear and decreased hearing. She denies ear discharge. She endorses vertigo for 7 months that is precipitated by sudden changes in head position. On physical exam, the right ear canal is obscured by a foreign body. Ear swab is positive for growth on fungal culture.

Lab Identification

Image 1. Salt and pepper fungal colonies isolated from ear swab.

aspniger — Image 1. Salt and pepper fungal colonies isolated from ear swab.

aspniger2 — Image 2. Septate hyphae with unbranched condidiophore connected to a swollen vesicle covered in phialides that produce chains of conidia.

The identification of Aspergillus niger is made based on macroscopic colony morphology and microscopic structures. On the potato flake agar, Aspergillus niger grows salt and pepper colonies. For microscopic examination, a slide is made by touching the colonies with a piece of clear tape, putting a drop of lactophenol analine blue on a glass slide, and placing the tape on the slide. Microscopically, Aspergillus niger appears as septate hyphae with long smooth unbranched conidiophores. Compared with other Aspergillus species, the phialides of niger cover the entire vesicle and form a “radiate” head, which splits into several loose columns.

Discussion

Aspergillus is a common mold that lives both indoors and outdoors. The Aspergillus genus is composed of 180 species, among which 34 are associated with human disease.¹ A. fumigatus is the most common cause of aspergillosis syndromes. A. terreus is a species of particular concern due to its resistance to amphotericin. An invasive disease due to A. terreus has a poor prognosis.¹

Healthy individuals inhale hundreds of conidia of Aspergillus per day without illness. However, people with a weakened immune system or lung disease are at higher risk of developing infections from inhaling the condidia. Presentations of aspergillosis range from allergy to fungal balls, to dissemination.¹ Examples of aspergillosis include asthma, allergic bronchopulmonary aspergillosis, and allergic sinusitis.¹

Invasive otitis externa due to Aspergillus is a rare, potentially life-threatening invasive fungal infection affecting immunocompromised patients.² It spreads from the external auditory canal to adjacent anatomical structures such as soft tissues, cartilage, and bone.² The condition can lead to osteomyelitis of the base of the skull with progressive cranial nerve palsies, irreversible hearing, and neurological impairment.² The infection can be treated with antifungals.

References

Barnes PD, Marr KA. Aspergillosis: spectrum of disease, diagnosis, and treatment. Infect Dis Clin North Am. 2006 Sep;20(3):545-61, vi.
Parize, P. et al. Antifungal Therapy of Aspergillus Invasive Otitis Externa: Efficacy of Voriconazole and Review. Antimicrobial agents and chemotherapy. 2018 April; 62(4). http://aac.asm.org/content/53/3/1048.long

-Ting Chen, MD is a 1^st year anatomic and clinical pathology resident at the University of Vermont Medical Center.

Wojewoda-small

-Christi Wojewoda, MD, is the Director of Clinical Microbiology at the University of Vermont Medical Center and an Associate Professor at the University of Vermont.