Major impacts of widespread structural variation on sorghum

Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in genome-wide selection, is not yet understood. In this study, we built an SV data set based on whole-genome resequencing of diverse sorghum lines (n = 363), validated the correlation of photoperiod sensitivity and variety type, and identified SV hotspots underlying the divergent evolution of cellulosic and sweet sorghum. In addition, we showed the complementary contribution of SVs for heritability of traits related to sorghum adaptation. Importantly, inclusion of SV polymorphisms in association studies revealed genotype-phenotype associations not observed with SNPs alone. Three-way genome-wide association studies (GWAS) based on whole-genome SNP, SV, and integrated SNP + SV data sets showed substantial associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the genome level. Our discovery of the widespread impacts of SVs on heritable gene expression variation could render a plausible mechanism for their disproportionate impact on phenotypic variation. This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum.

Comparing Deep Learning Approaches for Understanding Genotype × Phenotype Interactions in Biomass Sorghum

We explore the use of deep convolutional neural networks (CNNs) trained on overhead imagery of biomass sorghum to ascertain the relationship between single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the phenotypes they control. We consider both CNNs trained explicitly on the classification task of predicting whether an image shows a plant with a reference or alternate version of various SNPs as well as CNNs trained to create data-driven features based on learning features so that images from the same plot are more similar than images from different plots, and then using the features this network learns for genetic marker classification. We characterize how efficient both approaches are at predicting the presence or absence of a genetic markers, and visualize what parts of the images are most important for those predictions. We find that the data-driven approaches give somewhat higher prediction performance, but have visualizations that are harder to interpret; and we give suggestions of potential future machine learning research and discuss the possibilities of using this approach to uncover unknown genotype × phenotype relationships.

Nighttime Chlorophyll Fluorescence Imaging of Dark-Adapted Plants Using a Robotic Field Phenotyping Platform

Photosynthetic efficiency is increasingly recognized as an integration of plant responses to dynamic environments, establishing the need for data sets from both field trials and controlled environments. A robotic field scanner phenotyping platform at the University of Arizona is equipped with a high-throughput chlorophyll fluorescence imaging system capable of collecting data on field trials for genetic studies of a photosynthetic trait (Fv/Fm). A description of the fluorescence imaging system is provided in addition to methods for measurements across experimental field plots and a test to determine the impact of variable plant heights. The overall focus is on aspects of field applications of a chlorophyll fluorescence imaging system that differ from analogous systems in controlled environments.

Wireless Fixed Camera Network for Greenhouse-Based Plant Phenotyping

An indoor wireless fixed camera network was developed for an efficient, cost-effective method of extracting informative plant phenotypes in a controlled greenhouse environment. Deployed at the Donald Danforth Plant Science Center (DDPSC), this fixed camera platform implements rapid and automated plant phenotyping. The platform uses low-cost Raspberry Pi computers and digital cameras to monitor aboveground morphological and developmental plant phenotypes. The Raspberry Pi is a readily programmable, credit card-sized computer board with remote accessibility. A standard camera module connects to the Raspberry Pi computer board and generates eight-megapixel resolution images. With a fixed array, or "bramble," of Raspberry Pi computer boards and camera modules placed strategically in a greenhouse, we can capture automated, high-resolution images for 3D reconstructions of individual plants on timescales ranging from minutes to hours, capturing temporal changes in plant phenotypes.

Genetic characterization of a Sorghum bicolor multiparent mapping population emphasizing carbon-partitioning dynamics

Sorghum bicolor, a photosynthetically efficient C₄ grass, represents an important source of grain, forage, fermentable sugars, and cellulosic fibers that can be utilized in myriad applications ranging from bioenergy to bioindustrial feedstocks. Sorghum’s efficient fixation of carbon per unit time per unit area per unit input has led to its classification as a preferred biomass crop highlighted by its designation as an advanced biofuel by the U.S. Department of Energy. Due to its extensive genetic diversity and worldwide colonization, sorghum has considerable diversity for a range of phenotypes influencing productivity, composition, and sink/source dynamics. To dissect the genetic basis of these key traits, we present a sorghum carbon-partitioning nested association mapping (NAM) population generated by crossing 11 diverse founder lines with Grassl as the single recurrent female. By exploiting existing variation among cellulosic, forage, sweet, and grain sorghum carbon partitioning regimes, the sorghum carbon-partitioning NAM population will allow the identification of important biomass-associated traits, elucidate the genetic architecture underlying carbon partitioning and improve our understanding of the genetic determinants affecting unique phenotypes within Poaceae. We contrast this NAM population with an existing grain population generated using Tx430 as the recurrent female. Genotypic data are assessed for quality by examining variant density, nucleotide diversity, linkage decay, and are validated using pericarp and testa phenotypes to map known genes affecting these phenotypes. We release the 11-family NAM population along with corresponding genomic data for use in genetic, genomic, and agronomic studies with a focus on carbon-partitioning regimes.

Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation

Genomic structural mutations, especially deletions, are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum [Sorghum bicolor (L.) Moench] is one of the most widely grown cereal crops in the world. It has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity. In this study, we identified genome-wide SVs in the Biomass Association Panel, a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole-genome resequencing data from every genotype, we found a total of 24,648 SVs, including 22,359 deletions. The global site frequency spectrum of deletions and other types of SVs fit a model of neutral evolution, suggesting that the majority of these mutations were not under any types of selection. Clustering results based on single nucleotide polymorphisms separated the genotypes into eight clusters which largely corresponded with geographic origins, with many of the large deletions we uncovered being unique to a single cluster. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic and abiotic stress responses, supporting the possibility that at least some of these deletions contribute to local adaptation in sorghum.

Escalation in the host-pathogen arms race: A host resistance response corresponds to a heightened bacterial virulence response

The zig-zag model of host-pathogen interaction describes the relative strength of defense response across a spectrum of pathogen-induced plant phenotypes. A stronger defense response results in increased resistance. Here, we investigate the strength of pathogen virulence during disease and place these findings in the context of the zig-zag model. Xanthomonas vasicola pv. holcicola (Xvh) causes sorghum bacterial leaf streak. Despite being widespread, this disease has not been described in detail at the molecular level. We divided diverse sorghum genotypes into three groups based on disease symptoms: water-soaked lesions, red lesions, and resistance. Bacterial growth assays confirmed that these three phenotypes represent a range of resistance and susceptibility. To simultaneously reveal defense and virulence responses across the spectrum of disease phenotypes, we performed dual RNA-seq on Xvh-infected sorghum. Consistent with the zig-zag model, the expression of plant defense-related genes was strongest in the resistance interaction. Surprisingly, bacterial virulence genes related to the type III secretion system (T3SS) and type III effectors (T3Es) were also most highly expressed in the resistance interaction. This expression pattern was observed at multiple time points within the sorghum-Xvh pathosystem. Further, a similar expression pattern was observed in Arabidopsis infected with Pseudomonas syringae for effector-triggered immunity via AvrRps4 but not AvrRpt2. Specific metabolites were able to repress the Xvh virulence response in vitro and in planta suggesting a possible signaling mechanism. Taken together, these findings reveal multiple permutations of the continually evolving host-pathogen arms race from the perspective of host defense and pathogen virulence responses.

The arms race between plants and pathogens is a complex process. To dissect the plant defense and pathogen virulence responses simultaneously, we used sorghum and Xanthomonas vasicola pv. holcicola, as a model pathosystem. We performed dual RNA-seq on infected sorghum with a range of disease phenotypes. Our characterization of this pathosystem demonstrates that genes related to the plant defense and pathogen virulence responses are most highly induced during a resistance interaction. We observed a similar pattern of escalation in Arabidopsis infected with Pseudomonas syringae. These observations support a conceptual model of fluidity between the different stages of plant immunity and pathogen virulence.

Comparative evolutionary genetics of deleterious load in sorghum and maize

Sorghum and maize share a close evolutionary history that can be explored through comparative genomics^1,2. To perform a large-scale comparison of the genomic variation between these two species, we analysed ~13 million variants identified from whole-genome resequencing of 499 sorghum lines together with 25 million variants previously identified in 1,218 maize lines. Deleterious mutations in both species were prevalent in pericentromeric regions, enriched in non-syntenic genes and present at low allele frequencies. A comparison of deleterious burden between sorghum and maize revealed that sorghum, in contrast to maize, departed from the domestication-cost hypothesis that predicts a higher deleterious burden among domesticates compared with wild lines. Additionally, sorghum and maize population genetic summary statistics were used to predict a gene deleterious index with an accuracy greater than 0.5. This research represents a key step towards understanding the evolutionary dynamics of deleterious variants in sorghum and provides a comparative genomics framework to start prioritizing these variants for removal through genome editing and breeding.

PROHIBITIN3 Forms Complexes with ISOCHORISMATE SYNTHASE1 to Regulate Stress-Induced Salicylic Acid Biosynthesis in Arabidopsis

Salicylic acid (SA) is a major defense signal in plants. In Arabidopsis (Arabidopsis thaliana), the chloroplast-localized isochorismate pathway is the main source of SA biosynthesis during abiotic stress or pathogen infections. In the first step of the pathway, the enzyme ISOCHORISMATE SYNTHASE1 (ICS1) converts chorismate to isochorismate. An unknown enzyme subsequently converts isochorismate to SA. Here, we show that ICS1 protein levels increase during UV-C stress. To identify proteins that may play roles in SA production by regulating ICS1, we analyzed proteins that coimmunoprecipitated with ICS1 via mass spectrometry. The ICS1 complexes contained a large number of peptides from the PROHIBITIN (PHB) protein family, with PHB3 the most abundant. PHB proteins have diverse biological functions that include acting as scaffolds for protein complex formation and stabilization. PHB3 was reported previously to localize to mitochondria. Using fractionation, protease protection, and live imaging, we show that PHB3 also localizes to chloroplasts, where ICS1 resides. Notably, loss of PHB3 function led to decreased ICS1 protein levels in response to UV-C stress. However, ICS1 transcript levels remain unchanged, indicating that ICS1 is regulated posttranscriptionally. The phb3 mutant displayed reduced levels of SA, the SA-regulated protein PR1, and hypersensitive cell death in response to UV-C and avirulent strains of Pseudomonas syringae and, correspondingly, supported increased growth of P. syringae The expression of a PHB3 transgene in the phb3 mutant complemented all of these phenotypes. We suggest a model in which the formation of PHB3-ICS1 complexes stabilizes ICS1 to promote SA production in response to stress.

High throughput phenotyping to accelerate crop breeding and monitoring of diseases in the field

Effective implementation of technology that facilitates accurate and high-throughput screening of thousands of field-grown lines is critical for accelerating crop improvement and breeding strategies for higher yield and disease tolerance. Progress in the development of field-based high throughput phenotyping methods has advanced considerably in the last 10 years through technological progress in sensor development and high-performance computing. Here, we review recent advances in high throughput field phenotyping technologies designed to inform the genetics of quantitative traits, including crop yield and disease tolerance. Successful application of phenotyping platforms to advance crop breeding and identify and monitor disease requires: (1) high resolution of imaging and environmental sensors; (2) quality data products that facilitate computer vision, machine learning and GIS; (3) capacity infrastructure for data management and analysis; and (4) automated environmental data collection. Accelerated breeding for agriculturally relevant crop traits is key to the development of improved varieties and is critically dependent on high-resolution, high-throughput field-scale phenotyping technologies that can efficiently discriminate better performing lines within a larger population and across multiple environments.

Whole-Plant Manual and Image-Based Phenotyping in Controlled Environments

Phenotypic measurements and images of crops grown under controlled-environment conditions can be analyzed to compare plant growth and other phenotypes from diverse varieties. Those demonstrating the most favorable phenotypic traits can then be used for crop improvement strategies. This article details a protocol for image-based root and shoot phenotyping of plants grown in the greenhouse to compare traits among different varieties. Diverse maize lines were grown in the greenhouse in large 8-gallon treepots in a clay granule substrate. Replicates of each line were harvested at 4 weeks, 6 weeks, and 8 weeks after planting to capture developmental information. Whole-plant phenotypes include biomass accumulation, ontogeny, architecture, and photosynthetic efficiency of leaves. Image analysis was used to measure leaf surface area and tassel size and to extract shape variance information from complex 3D root architectures. Notably, this framework is extensible to any number of above- or below-ground phenotypes, both morphological and physiological. © 2017 by John Wiley & Sons, Inc.

Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition

Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. The identification of genes and alleles that modify element content in the grains of cereals, including sorghum (Sorghum bicolor), is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high-throughput work flow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel, representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome-wide association was demonstrated by implementing rank transformation and a multilocus mixed model to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc, manganese, nickel, calcium, and cadmium in sorghum seeds. In addition to strong candidates for these five elements, we provide a list of candidate loci for several other elements. Our approach enabled the identification of single-nucleotide polymorphisms in strong linkage disequilibrium with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement.

Vibratory sense deficits in patients with symptomatic femoroacetabular impingement

OBJECTIVE

Sensory deficits, measured through vibratory perception threshold (VPT), have been recognized in hip and knee osteoarthritis (OA), but have not been evaluated in femoroacetabular impingement (FAI), thought to be a pre-OA condition. This study aimed to assess VPT in symptomatic FAI pre- and 6-months post-arthroscopy vs.

METHODS

FAI patients and controls were assessed for VPT at the first metatarsophalangeal joint. Pain was assessed using a visual analog pain scale. FAI participants were evaluated again 6-months after surgery for FAI. Differences between groups and pre- and post- surgery were evaluated with independent and paired sample t-tests, respectively. Secondary analysis was performed using repeated-measures ANOVA to evaluate the effect of pain and time since surgery on VPT pre- and post-operatively.

RESULTS

No differences in age and BMI were seen between groups (p>0.05). Reduced VPT (higher value is worse) was evident in the pre- (8.0±3.9V, t=2.81, p=0.009) and post-operative (6.8±2.8V, t=2.34, p=0.027) patients compared to controls (4.7±1.3V). After hip arthroscopy, there was a trend toward improved VPT (t=1.97, p=0.068). Preoperative and 6-months postoperative pain and time since surgery were not found to influence VPT (F-ratio⋝0.00, p⋝0.427).

CONCLUSION

Sensory deficits were observed in FAI patients both before and 6-months after hip arthroscopy.

A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

BACKGROUND

Effective improvement in sorghum crop development necessitates a genomics-based approach to identify functional genes and QTLs. Sequenced in 2009, a comprehensive annotation of the sorghum genome and the development of functional genomics resources is key to enable the discovery and deployment of regulatory and metabolic genes and gene networks for crop improvement.

RESULTS

This study utilizes the first commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast, and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (maize and sugarcane) were also included in our array design. We generated expression data for 78 samples with a combination of four different tissue types (shoot, root, leaf and stem), two dissected stem tissues (pith and rind) and six diverse genotypes, which included 6 public sorghum lines (R159, Atlas, Fremont, PI152611, AR2400 and PI455230) representing grain, sweet, forage, and high biomass ideotypes.

CONCLUSIONS

Here we present a summary of the microarray dataset, including analysis of tissue-specific gene expression profiles and associated expression profiles of relevant metabolic pathways. With an aim to enable identification and functional characterization of genes in sorghum, this expression atlas presents a new and valuable resource to the research community.

The biomechanical effects of focused muscle training on medial knee loads in OA of the knee: a pilot, proof of concept study

BACKGROUND

High dynamic loads of the medial knee are associated with tibiofemoral osteoarthritis (OA) severity and progression. The lower extremity acts as an integrated kinetic unit, thus treatments targeting adjacent segments may promote reductions in the loading of a symptomatic knee. This study examined the biomechanical effects of a lower extremity exercise regimen, emphasizing training of hip abductor musculature, on dynamic knee loads in individuals with knee OA.

METHODS

Six subjects with medial compartment knee OA participated in a proof of concept study of a four-week exercise program specifically targeting the hip abductor musculature in combination with traditional quadriceps and hamstring training. Assessments included gait analyses to measure the external knee adduction moment, a surrogate marker of medial knee joint loading as well as WOMAC questionnaires and strength evaluations.

RESULTS

All subjects demonstrated a decrease in their external knee adduction moment, with an average decrease of 9% (p<0.05) following the exercise intervention. There was a 78% (p<0.05) decrease in WOMAC knee pain scores.

CONCLUSIONS

These results suggest that targeting hip, rather than only knee musculature, may represent an effective biomechanically-based treatment option for medial knee OA.

Pain and its relationship with muscle strength and proprioception in knee OA: results of an 8-week home exercise pilot study

Muscle strength and proprioception deficits have been recognized in knee OA. Pain is the symptomatic hallmark of knee OA. Indirect evidence suggests that muscle strength and proprioception deficits may be interrelated and that pain may have a confounding influence on the measurement of these factors in knee OA. However, these relationships have never been clearly evaluated. Therefore, the purpose of this investigation was to investigate relationships between pain, muscle strength, and proprioception in subjects with knee OA before and after an 8-week home exercise program. This study evaluated thirty-eight subjects with knee OA. Subjects were taught standard quadriceps strengthening exercises that were to be performed daily at home. Pain, muscle strength, and proprioceptive function were measured at baseline and after 8 weeks of therapy. Significant improvements in pain (42%, p<0.001) and quadriceps muscle strength (30%, p<0.001) were noted. Significant indirect associations were observed between pain and both muscle strength (rho=-0.39, p=0.01) and proprioceptive acuity (rho=-0.35, p=0.03) at baseline. Changes in pain were directly associated with changes in muscle strength (rho=0.45, p=0.005) and proprioceptive acuity (rho=0.41, p=0.01) with exercise. The association of pain with both muscle strength and proprioception should prompt future studies to consider and adjust for the influence of pain on neuromuscular factors in knee OA.

Allogeneic peripheral blood stem cell transplantation in patients with haematological malignancies

OBJECTIVE

To report the initial data on allogeneic peripheral blood stem cell transplantation for haematological malignancies in Pakistan.

DESIGN

A single centre descriptive study.

PLACE AND DURATION OF STUDY

Bismillah Taqee Institute of Health Sciences and Blood Diseases Centre from September 1999 to June 2004.

PATIENTS AND METHODS

Patients with haematological malignancies were included who had received allogeneic PBSC transplantation of Filgrastim (rhG-CSF) mobilized peripheral blood stem cells from HLA-identical siblings (except one 5/6 antigen sibling) with Busulphan and Cyclophosphamide standard conditioning therapy in all patients. No patient received antibiotics for gut decontamination. Empirical antibiotics included Ceftriaxone and Amikacin for febrile neutropenia, oral Itraconazole for antifungal prophylaxis while oral acyclovir was used for antiviral prophylaxis. All donors and recipients were CMV IgG positive Cyclosporin A / Methotrexate were given for graft versus host disease (GvHD) prophylaxis. Stem cells were harvested using Haemonetics MCS+ cell separator. All patients received G-CSF starting from day +4 until their neutrophil count rose to normal.

RESULTS

There were 21 patients with age range of 8-38 years and male to female ratio of 2:1. Engraftment was achieved in all patients; median time to absolute neutrophil count of > 0.5 x 10(9)/l was 10 days (range 8 - 12 days) and platelet count of > 20 x 10(9)/l was 14 days (12-17 days). Acute graft versus host disease ( aGvHD) was seen in 7 patients; one patient had grade IV skin and hepatic GvHD; another patient had grade III gut GvHD, grade II GvHD was seen in 3 patients while grade I skin aGvHD was seen in 2 patients. Median hospital stay was 34 days. Treatment related mortality was seen in 3 patients (18%). Chronic GvHD was seen in 5 patients. Four more patients died during the follow-up period. Malaria was seen in 2 while tuberculosis developed in one case. Relapse was seen in 2 patients. The estimated probability of survival at one hundred day, at one year and five years was 82, 47 and 40 percent respectively.

CONCLUSION

Haematopoietic stem cell transplant programme can be developed in a developed country setting. Post transplant complications are similar to what have been reported in the developed countries. In endemic areas malaria could prove to be fatal if not recognised and treated early.

Allogeneic peripheral blood stem cell transplantation for aplastic anaemia: a single centre experience

OBJECTIVE

To assess the feasibility of stem cell transplantation in local setting.

SETTING

A tertiary care haematology centre.

STUDY DESIGN

This is a single centre retrospective analysis of the outcome of allogeneic peripheral blood stem cell transplantation for severe aplastic anaemia.

OBJECTIVES

Preliminary data on stem cell transplantation in Pakistan.

PATIENTS AND METHODS

Aplastic anaemia is an uncommon disorder with a high mortality without treatment. Immunosuppression and bone marrow transplantation remains the mainstay of treatment. Stem cell transplantation facility became available in Pakistan in 1999, since then both allogeneic and autologous procedures are carried out for severe aplastic anaemia, b-thalassaemia major and haematological malignancies. Between April 2000 and July 2002, 20 allogeneic peripheral blood stem cell transplants were carried out for aplastic anaemia from HLA identical siblings. Donors were primed with G-CSF 10 mcg/kg/day subcutaneously for 4 days; stem cells were harvested on 5th day using Haemonetics MCS+ cell separator. Cyclophosphamide was used for conditioning; cyclosporin A and methotrexate were given for graft versus host disease prophylaxis.

RESULTS

Eighteen out of 22 patients survived transplant in a follow up period of 788 days. The causes of death were intra-cranial haemorrhage on day +7, herpes encephalitis on day +180, graft failure and mucour mycosis on day +353 and TB meningitis on day +544. Allogeneic peripheral blood stem cell transplantation resulted in 81% event free survival in our hands.

CONCLUSION

Allogeneic peripheral blood stem cell transplantation is feasible and life saving in an otherwise fatal disorder. This could be carried out effectively in Pakistan.

Peripheral blood stem cell transplantation in children with beta-thalassemia major

OBJECTIVE

To share the preliminary data on stem cell transplantation in Pakistan.

DESIGN

This is a single center retrospective analysis of the outcome of allogeneic peripheral blood stem cell (PBSC) transplantation in b-thalassemia major patients.

PLACE AND DURATION OF STUDY

Bismillah Taqee Blood Diseases Centre, Karachi; a tertiary care hematology center from September 1999 to September 2002.

PATIENTS AND METHODS

Twelve patients with b-thalassemia major received allogeneic PBSC transplantation from HLA identical sibling donors except in one case where mother was the donor. All patients received busulphan and cyclophosphamide conditioning therapy and cyclosporin A/methotrexate for graft versus host disease (GVHD) prophylaxis. Donors were primed with G-CSF for 4 days and stem cells were harvested using Haemonetics MCS + cell separator on 5th day. All patients received G-CSF starting from day + 4 until their neutrophil count rose to normal.

RESULTS

Engraftment was achieved in all patients except one who required a second dose of bone marrow graft on day +21. Median time to achieve absolute neutrophil count of > 0.5 x 10(9)/l was 9.0 days (range 8-31 days) and platelet count of > 20 x 10(9)/l was 14 days (12-35 days). Acute GVHD was seen in 3 patients, one patient had grade IV gut GVHD; another patient had grade III gut GVHD while third patient had grade II skin GVHD. Median hospital stay was 29 days. Six patients were well and transfusion independent 3 to 36 months posttransplant. One episode of primary graft failure required a second dose of bone marrow harvest. Another episode of graft rejection received two doses of donor lymphocytes infusion. There were 4 deaths due to grade IV gut GVHD because of uncontrolled systemic Candida infection and one due to hepatic veno-occlusive (VOD) disease.

CONCLUSION

Allogeneic peripheral blood stem cell transplantation can be safely and economically carried out in Pakistan. Although there had been 4 deaths during 36 months follow-up, with increasing understanding and experience the outcome is expected to improve.