Aplastic Anemia

A 3-year old female patient, born as an only child to non-consanguineous parents of Turkish descent after an uncomplicated pregnancy and delivery, presented with profound early-onset developmental delay, microcephaly, seizures, dysmorphic features, myopia, bone marrow dysplasia with lymphopenia, neutropenia, aplastic anemia and combined immunodeficiency (B and T cell) was enrolled into the TIDEX gene discovery project, approved by the Ethics Board of the Faculty of Medicine of the University of British Columbia (H12-00067).
Extensive clinical investigations were performed according to the TIDE diagnostic protocol [35 (link)] to determine the etiology of patient’s condition. These included: chromosome micro array analysis for copy number variants (CNVs) (Affymetrix Genome-Wide Human SNP Array 6.0); telomere length analysis; CT and MRI scans and comprehensive metabolic testing.
Genomic DNA was isolated from the peripheral blood of the patient as well as parents using standard techniques. Whole exome sequencing was performed for the index patient and her unaffected parents using the Ion AmpliSeq™ Exome Kit and Ion Proton™ System from Life Technologies (Next Generation Sequencing Services, UBC, Vancouver, Canada) at 120X coverage. An in-house designed bioinformatics pipeline (Additional file 7: Text S3) was used to align the reads to the human reference genome version hg19 and to identify and assess rare variants for their potential to disrupt protein function. The candidate variants were further confirmed using Sanger re-sequencing in all the family members. Primer sequences and PCR conditions are available on request. Deleteriousness of the candidate variants was assessed using Combined Annotation–Dependent Depletion (CADD) scores [36 (link)].

The NIH Office of Human Subject Research Protection (OHSRP) approved the study. The study was performed in a de-identified and anonymized manner, i.e. did not include patient names or medical record numbers, thus, written consent was waved by the OHSRP. The packet of questionnaires included an informed consent sheet that described the study, the purpose of the study, the voluntary nature of the participation, the nature of the information requested, the approximate time it takes to complete the questionnaires, and an explicit explanation that declining to participate did not affect the patient’s care at the NIH Clinical Center (S1 File). The Consent Information also included contact information for one of the investigators (RA) in case of additional questions or concerns. If the patient verbally consented to participate, then a numbered packet of self-report questionnaires was given to the participant. PPCS staff and two Special Volunteers received in-service from PPCS research staff (AB, RA, MJL, JHC) regarding the project. A PPCS representative, i.e. research associates (MJL, JHC), PPCS clinicians, or one of the two Special Volunteers, approached the patients in several Clinical Center hospital units and Outpatient clinics while the patients were in their hospital rooms or waiting for their medical appointments in outpatient clinics. The PPCS representative first verbally described the study and if the patient expressed interest, they were presented with the written Consent Information and the packet of questionnaires. PPCS representatives were available while patients completed the questionnaires. All patients were already involved in experimental treatments and research projects for the study and treatment of their particular disease at the NIH Clinical Center. They were in various stages of their treatment and recovery. Some patients were in remission in response to the investigative treatments. Two hundred consecutive NIH Clinical Center patients involved in experimental clinical research who consented to participate, were included in this current study. The recruitment took place from June to December of 2017.The eligibility criteria for this study included age of 18 or above, the ability to read and write in English, and the presence or history of a serious and/or life-threatening disease. These included but were not limited to various forms of advanced/metastatic cancer in one or several organs (e.g. lung, liver, pancreas, thyroid, thymus, ovaries, prostate, colon, stomach, kidney, blood, brain, and skin), blood dyscrasias (e.g. sickle cell anemia, aplastic anemia), graft vs. host disease (GVHD), as well as severe and rare genetic conditions (e.g. Camurati-Englemann Disease, Carney Complex Disease, Familial Dysautonomia, Job’s Syndrome, von Hippel-Lindau Disease, Myelodysplastic Syndrome, Neuromyelitis Optic or Devic’s Syndrome, Neurofibromatosis). Table 1 summarizes patient demographics by self-report including gender, age, race/ethnicity, marital status, religious affiliation, education, employment status, medical diagnosis, estimated duration of illness, the patient’s perception of their current severity of their illness, psychiatric comorbidity, perceived stress level, perceived level of social support, overall health status, and overall quality of life (S2 File).

Wherever appropriate, the absolute numbers of transplanted patients, number of transplants or transplant rates are shown for specific countries, indications, or transplant techniques. Myeloid malignancy include acute myeloid leukemia (AML), myelodysplastic or myelodysplastic/myeloproliferative neoplasia (MDS or MDS/MPN overlap), myeloproliferative neoplasm (MPN), and chronic myeloid leukemia (CML). Lymphoid malignancy include acute lymphocytic leukemia (ALL), chronic lymphocytic leukemia (CLL), Hodgkin lymphoma (HL), non-Hodgkin lymphoma (NHL) and plasma cell disorders (PCD) (including multiple myeloma (MM) and others). Non-malignant disorders include bone marrow failure (BMF: severe aplastic anemia (SAA) and other BMF), thalassemia and sickle cell disease (HG), primary immune deficiencies (PID), inherited diseases of metabolism (IDM), and autoimmune diseases (AID). Others include histiocytosis and other rare disorders.

The data of newly diagnosed AA patients in the First Affiliated Hospital of Zhejiang Chinese Medical University from January 2019 to July 2021 were retrospectively reviewed. The diagnosis and assessment of the disease were confirmed based on the Camitta criteria [11 (link)] and 2015 BJH guidelines [12 (link)], and the cases included severe aplastic anemia (SAA), very severe aplastic anemia (VSAA), non-severe aplastic anemia (NSAA), and transfusion-dependent none-severe aplastic anemia (TD-NSAA). Informed consent was obtained according to the Helsinki Declaration. This study was also registered at chictr.org.cn (# ChiCTR2100054992).

In total, 361,322 individuals from the UKB and 3,971 individuals from a Chinese population were included in our study (Figure 1). The UKB is a prospective cohort study with a large amount of genetic and phenotypic data collected from approximately 500,000 individuals across the United Kingdom from 2006 to 2010 (20 (link)–22 (link)). Patients with psoriasis were included from primary care, hospital admission, self-reports, and other sources in the UKB (Table S1). Participants were excluded from the UKB dataset based on the following criteria: it did not pass quality control of genotypic data (missing information on individual data > 0.02, sex discrepancy, and deviates of more than ±3 standard deviations (SD) from the heterozygosity rate mean of the samples); kinship >first-degree relationship; genetic ethnic grouping showed non-Caucasian (defined by data-field: 22,006 from UKB based on a principal components analysis of the genotypes) (23 (link)); suffering from diseases of the blood and hematopoietic system including leukemia, lymphoma, multiple myeloma, aplastic anemias, and agranulocytosis, among others (Table S1); and a white blood cell count >200 × 10⁹ cells/L (24 (link)). The Chinese population included patients with psoriasis admitted to Xiangya Hospital, Central South University between 2019 and 2020. Patients with diseases of the blood and hematopoietic system and abnormal white blood cell count (>200 × 10⁹ cells/L) were excluded. The diagnosis of psoriasis in the Chinese population was confirmed by two or more dermatologists. The UKB received ethical approval from the Northwest Multi-Center Research Ethics Committee (11/NW/03820). All procedures involving study participants in the Chinese population were approved by the institutional research ethics board of Xiangya Hospital (2018121106). Written informed consent was obtained from all participants prior to the investigation.